Browse the workbook contents

Collection size: 203

Structured List

article

Data Science Principles

article

Applications of Computational Science

intro

Computational Biology

intro

Geospatial Analytics

intro

Machine Learning

article

Operating System (OS) installation

tutorial

Getting started with macOS

tutorial

Windows command-line environments

tutorial

Automated batch file operations on Windows

tutorial

Configuring your Linux system

intro

Must-have software

article

Basic office software

article

Basic developer tools

article

Basic developer libraries

intro

Various methods of software installation

tutorial

Installations on MacBook Pro

tutorial

Installations on Windows

tutorial

Installations on Linux

tutorial

Terminal - an interface for command-line operations

tutorial

Introduction to UNIX Shell: configuration, variables, home dir

tutorial

Basic Commands: navigation, file creation & preview

tutorial

Command Line text files editors: nano, vim

tutorial

System info and access permissions

tutorial

Superuser command: sudo

tutorial

Getting started with UNIX + video + exercises

intro

Useful text manipulation programs

tutorial

GREP – simple search for regular expressions

tutorial

SED – replace pattern in stream text

tutorial

AWK – advanced text processing

tutorial

BIOAWK – biological data manipulation

tutorial

DIFF, COMM, CMP – comparing and collating two files with Unix

cheatsheet

UNIX Commands

intro

Integrated & Interactive Development Environment (IDE)

tutorial

Visual Studio Code: multi-language integrated DE (VSC)

tutorial

Jupyter: interactive web-based multi-kernel DE

tutorial

Getting started with JupyterLab on a local machine

tutorial

Getting started with Jupyter Notebook on HPC systems

tutorial

Sharing Jupyter-based reproducible pipline via MyBinder

intro

Python programming environment(s)

tutorial

Online Console: simple Python code in a browser (without installation)

tutorial

Online Notebook: interactive Python on Try-jupyter and Colab (no installation)

tutorial

Local Python setup on your computing machine (installation needed)

tutorial

Shell & IDLE: Python code in a terminal or simple IDE (beginner)

tutorial

Text editors: create Python code in terminal text files (intermediate)

tutorial

Jupyter Lab: create an interactive Python notebook (advanced)

tutorial

PyCharm: IDE for professional Python developers (professional)

intro

R programming environment(s)

tutorial

RStudio: integrated environment for R programming

tutorial

Setting up RStudio

intro

Basics of Algorithm Structure

tutorial

Introduction to Bash scripting

tutorial

Process multiple files

tutorial

Introduction to regular expression

tutorial

Introduction to Python programming

tutorial

Open-Close & Read-Write of data files

tutorial

JSON module - encoding & decoding JSON data

tutorial

Math module - various mathematical functions

tutorial

Pandas library - data structure manipulation tool

tutorial

NumPy library - multi-dimensional arrays parser

tutorial

SciPy library - algorithms for scientific computing

tutorial

Introduction to R programming

tutorial

Base R - core functionality for statistical computing

tutorial

Base R Graphics - traditional statistical graphing

tutorial

ggplot2 - customizable graphs and charts

tutorial

dplyr - data manipulation and transformation

tutorial

tidyverse - advanced data manipulation, exploration and visualization

tutorial

data.table - aggregation and manipulation of large data sets

tutorial

Introduction to Julia programming

tutorial

Julia setup: installation, environments and Jupyter integration

intro

Introduction to HPC infrastructure

intro

ACCESS - an advanced computing and data resource program

tutorial

XSEDE supercell storage

intro

SCINet Scientific Computing: HPC, high-speed networking and training

tutorial

SCINet: Atlas computing cluster

tutorial

SCINet: Ceres computing cluster

tutorial

SCINet: Juno storage

intro

ISU HPC Network

tutorial

ISU HPC: Condo computing cluster

tutorial

ISU HPC: Nova computing cluster

tutorial

ISU HPC: LSS system

intro

Remote Access to HPC resources

tutorial

Virtual Private Network (VPN) Connection (command line)

tutorial

Secure Shell Connection (SSH) (command line)

tutorial

SSH shortcuts and password-less login

tutorial

Open On Demand (OOD) Connection (web-based GUI)

tutorial

Setting up your home directory for data analysis

tutorial

Example .bashrc file configuration

tutorial

Software Available on HPC

tutorial

Accessing pre-installed modules

tutorial

Accessing software via package manager

tutorial

Installing custom programs in user space

tutorial

Introduction to job scheduling

tutorial

SLURM: basics of workload manager

tutorial

Introduction to SLURM

cheatsheet

SLURM commands

tutorial

Creating SLURM job submission scripts

tutorial

Submitting dependency jobs using SLURM

tutorial

PBS: Portable Batch System

cheatsheet

PBS commands

tutorial

Creating PBS job submission scripts

tutorial

Submitting dependency jobs using PBS

tutorial

Introduction to GNU parallel

intro

Introduction to containers

tutorial

Apptainer: the container system for secure HPC (singularity rebranding)

tutorial

Singularity (archival)

tutorial

Creating containers using Singularity

tutorial

Modifying existing containers

tutorial

Singularity on your Mac via Vagrant

tutorial

Docker - accelerated container application development

tutorial

Remote data access

intro

Remote data transfer

tutorial

Copying Data using Graphical Interface: Globus

tutorial

Copying Data via SSH using Command Line: scp, rsync

tutorial

File transfer using irods

intro

Remote data download

tutorial

Downloading Online Data using WGET

tutorial

Downloading online data using API

tutorial

Downloading online data using Python-based web scraping

tutorial

Downloading online repos using GIT: [GitHub, Bitbucket, SourceForge]

tutorial

Downloading a single folder or file from GitHub

tutorial

Remote data preview (without downloading)

tutorial

Viewing text files using UNIX commands

tutorial

Viewing PDF and PNG files using X11 SSH connection

tutorial

Viewing graphics in a terminal as the text-based ASCII art

tutorial

Mounting remote folder on a local machine

intro

Data manipulation

intro

Manipulating Excel data sheets

tutorial

Create worksheet from multiple text files

tutorial

Export multiple worksheets as separate text files

tutorial

Create index for all worksheets

tutorial

Merge two spreadsheets using a common column

intro

Manipulating text files with Python

tutorial

Read, write, split, select data

tutorial

Data wrangling: use ready-made apps

tutorial

Merge files by common column (python)

tutorial

Aggregate data over slicing variations (python)

tutorial

Split data or create data chunks (python)

intro

Introduction to scientific graphic design

tutorial

Raster graphics tools

tutorial

Vector graphics tools

tutorial

Adobe creative cloud

tutorial

Template-based web tools

intro

Introduction to scientific graphing

tutorial

Gnuplot: creating plots in the UNIX Shell

tutorial

Gnuplot: variables, loops, conditionals

tutorial

Gnuplot: filled curves

tutorial

Plotly-Dash: interactive plotting with Python

tutorial

Introduction to Plotly (python)

tutorial

Introduction to Dash (python)

tutorial

Plotly graphing - interactive examples in the JupyterLab

tutorial

Creating XY scatter plot

tutorial

Creating 1D volcano plot

tutorial

Creating heatmap

tutorial

Creating dendrogram

tutorial

Creating clustergram

tutorial

RStudio – data processing & plotting with R

tutorial

Creating boxplots in R

tutorial

Creating heatmaps in R

tutorial

Creating heatmaps in R using ComplexHeatmap

article

Introduction to Project Management

intro

Overview of essential tools for modern research

article

Project strategy and risk management

tutorial

Project Design vs Project Framework

article

Collaboration & Communication

intro

Team communication tools

tutorial

Introduction to Slack

intro

Resource Management

intro

Data Management

tutorial

Open Science policy

tutorial

FAIR principles

tutorial

CARE principles

tutorial

TRUST principles

tutorial

Data Management Plan (hands-on)

intro

Code Development & Management

intro

Storage & Version Control

tutorial

GIT - a distributed version control system

cheatsheet

GIT Commands

intro

Online hosting platforms for GIT repositories

tutorial

Introduction to GitHub

tutorial

GitHub - getting started

tutorial

GitHub - getting started (class exercise)

tutorial

Introduction to BitBucket

intro

Documentation improvement tools

tutorial

A Practical guide to managing research documentation

tutorial

Tools for research documentation

tutorial

Tools for code documentation

tutorial

Introduction to Markdown

article

Quality Assurance

tutorial

Monitoring & Evaluation

tutorial

Enhancing productivity in research

tutorial

Reproducibility in research

tutorial

Research reproducibility guideline

intro

Project Closing

tutorial

Research Publication

Alphabetical List

• 01: Introduction to Data Science
• 02: Setting Up Computing Machine
• 03: Introduction to Command Line
• 04: Development Environment
• 05: Introduction to Programming
• 06: High-Performance Computing (HPC)
• 07: Data Acquisition and Wrangling
• 08: Data Visualization
• 09: Project Management
• Code Development & Management
• Data Management
• Documentation improvement tools
• Storage & Version Control
• A Practical guide to managing research documentation
• ACCESS - an advanced computing and data resource program
• AWK – advanced text processing
• Accessing pre-installed modules
• Accessing software via package manager
• Adobe creative cloud
• Aggregate data over slicing variations
• Applications of Computational Science
• Apptainer: the container system for secure HPC
• Automated batch file operations on Windows
• BIOAWK – biological data manipulation
• Base R - core functionality for statistical computing
• Base R Graphics - traditional statistical graphing
• Basic Commands: navigation, file creation & preview
• Basic developer libraries
• Basic developer tools
• Basic office software
• Basics of Algorithm Structure
• CARE principles
• Collaboration & Communication
• Command Line text files editors: nano, vim
• Computational Biology
• Configuring your Linux system
• Copying Data using Graphical Interface: Globus
• Copying Data via SSH using Command Line: scp, rsync
• Create index for all worksheets
• Create worksheet from multiple text files
• Creating 1D volcano plot
• Creating PBS job submission scripts
• Creating SLURM job submission scripts
• Creating XY scatter plot
• Creating boxplots in R
• Creating clustergram
• Creating containers using Singularity
• Creating dendrogram
• Creating heatmap
• Creating heatmaps in R
• Creating heatmaps in R using ComplexHeatmap
• DIFF, COMM, CMP – comparing and collating two files with Unix
• Data Management Plan
• Data Science Principles
• Data manipulation
• Data wrangling: use ready-made apps
• Docker - accelerated container application development
• Downloading Online Data using WGET
• Downloading a single folder or file from GitHub
• Downloading online data using API
• Downloading online data using Python-based web scraping
• Downloading online repos using GIT: [GitHub, Bitbucket, SourceForge]
• Enhancing productivity in research
• Example .bashrc file configuration
• Export multiple worksheets as separate text files
• FAIR principles
• File transfer using irods
• GIT - a distributed version control system
• GIT Commands
• GREP – simple search for regular expressions
• Geospatial Analytics
• Getting started with Jupyter Notebook on HPC systems
• Getting started with JupyterLab on a local machine
• Getting started with UNIX + video + exercises
• Getting started with macOS
• GitHub - getting started
• GitHub - getting started (class exercise)
• Gnuplot: creating plots in the UNIX Shell
• Gnuplot: filled curves
• Gnuplot: variables, loops, conditionals
• ISU HPC Network
• ISU HPC: Condo computing cluster
• ISU HPC: LSS system
• ISU HPC: Nova computing cluster
• Installations on Linux
• Installations on MacBook Pro
• Installations on Windows
• Installing custom programs in user space
• Integrated & Interactive Development Environment (IDE)
• Introduction to Bash scripting
• Introduction to BitBucket
• Introduction to Dash
• Introduction to GNU parallel
• Introduction to GitHub
• Introduction to HPC infrastructure
• Introduction to Julia programming
• Introduction to Markdown
• Introduction to Plotly
• Introduction to Project Management
• Introduction to Python programming
• Introduction to R programming
• Introduction to SLURM
• Introduction to Slack
• Introduction to UNIX Shell: configuration, variables, home dir
• Introduction to containers
• Introduction to job scheduling
• Introduction to regular expression
• Introduction to scientific graphic design
• Introduction to scientific graphing
• JSON module - encoding & decoding JSON data
• Julia setup: installation, environments and Jupyter integration
• Jupyter Lab: create an interactive Python notebook
• Jupyter: interactive web-based multi-kernel DE
• Local Python setup on your computing machine
• Machine Learning
• Manipulating Excel data sheets
• Manipulating text files with Python
• Math module - various mathematical functions
• Merge files by common column
• Merge two spreadsheets using a common column
• Modifying existing containers
• Monitoring & Evaluation
• Mounting remote folder on a local machine
• Must-have software
• NumPy library - multi-dimensional arrays parser
• Online Console: simple Python code in a browser
• Online Notebook: interactive Python on Try-jupyter and Colab
• Online hosting platforms for GIT repositories
• Open On Demand (OOD) Connection
• Open Science policy
• Open-Close & Read-Write of data files
• Operating System (OS) installation
• Overview of essential tools for modern research
• PBS commands
• PBS: Portable Batch System
• Pandas library - data structure manipulation tool
• Plotly graphing - interactive examples in the JupyterLab
• Plotly-Dash: interactive plotting with Python
• Process multiple files
• Project Closing
• Project Design vs Project Framework
• Project strategy and risk management
• PyCharm: IDE for professional Python developers
• Python programming environment(s)
• Quality Assurance
• R programming environment(s)
• RStudio – data processing & plotting with R
• RStudio: integrated environment for R programming
• Raster graphics tools
• Read, write, split, select data
• Remote Access to HPC resources
• Remote data access
• Remote data download
• Remote data preview
• Remote data transfer
• Reproducibility in research
• Research Publication
• Research reproducibility guideline
• Resource Management
• SCINet Scientific Computing: HPC, high-speed networking and training
• SCINet: Atlas computing cluster
• SCINet: Ceres computing cluster
• SCINet: Juno storage
• SED – replace pattern in stream text
• SLURM commands
• SLURM: basics of workload manager
• SSH shortcuts and password-less login
• SciPy library - algorithms for scientific computing
• Secure Shell Connection (SSH)
• Setting up RStudio
• Setting up your home directory for data analysis
• Sharing Jupyter-based reproducible pipline via MyBinder
• Shell & IDLE: Python code in a terminal or simple IDE
• Singularity
• Singularity on your Mac via Vagrant
• Software Available on HPC
• Split data or create data chunks
• Submitting dependency jobs using PBS
• Submitting dependency jobs using SLURM
• Superuser command: sudo
• System info and access permissions
• TRUST principles
• Team communication tools
• Template-based web tools
• Terminal - an interface for command-line operations
• Text editors: create Python code in terminal text files
• Tools for code documentation
• Tools for research documentation
• UNIX Commands
• Useful text manipulation programs
• Various methods of software installation
• Vector graphics tools
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Viewing text files using UNIX commands
• Virtual Private Network (VPN) Connection
• Visual Studio Code: multi-language integrated DE (VSC)
• Windows command-line environments
• XSEDE supercell storage
• data.table - aggregation and manipulation of large data sets
• dplyr - data manipulation and transformation
• ggplot2 - customizable graphs and charts
• tidyverse - advanced data manipulation, exploration and visualization

Filter by Category:

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Filter by tag Filter by tag aria-label="Filter by tag" 2D-plot 3D-plot GUI Google Charts Highcharts IDE OOD R SQL Tableau Public algorithm alias arithmetic bash binary-search bubble-sort code-editor comm common-divisor compiler control-flow custom-software debugger development-environment diff excel factorial file-compression filled-curves gnuplot graph-layout hpc-cluster in-browser inputs interface job-management join julia jupyter library linear-search linux local-machine logical-operator loop macOS machine-learning markdown mathplotlib module module-avail module-list module-load module-purge module-show notebook numerical-computing outputs package package-manager paste plot-data-from-file plot-math-formula plotly process-multiple-files pseudocode python raw-data regex regular-expression replace-pattern reproducibility reverse-string scientific scientific-computing script-file search-pattern sum syntax terminal variable windows workdir

• Jupyter: interactive web-based multi-kernel DE
• 05: Introduction to Programming
• Basics of Algorithm Structure
• Introduction to Bash scripting
• Process multiple files
• Introduction to regular expression
• Software Available on HPC
• Accessing pre-installed modules
• Data manipulation
• Introduction to scientific graphing
• Gnuplot: creating plots in the UNIX Shell
• Gnuplot: variables, loops, conditionals
• Gnuplot: filled curves

---

Filter by tag Filter by tag aria-label="Filter by tag" BitBucket CLI GUI GitHub Mercurial OneNote R SVN SciNote Slack artificial-intelligence backup backups bash binary code-archiving code-docs code-lifecycle code-release code-sharing code-storage code-testing collaboration command comments commit config count-files data-docs data-storage deadline docs-generator docstring eLabFTW file-list file-size git goals hosting-platform jupyter knowledge-retention local-repo manage-conflicts markdown note-taking notebook objectives productivity publication pull-updates push-changes python raw-data readme reference-manager remote-repo repository reproducibility source-code standards strategy subversion timeline workdir

• Code Development & Management
• Storage & Version Control
• GIT - a distributed version control system
• GIT Commands
• Online hosting platforms for GIT repositories
• Introduction to GitHub
• GitHub - getting started
• GitHub - getting started (class exercise)
• Introduction to BitBucket
• Documentation improvement tools
• A Practical guide to managing research documentation
• Tools for research documentation
• Tools for code documentation
• Quality Assurance
• Monitoring & Evaluation
• Enhancing productivity in research
• Reproducibility in research
• Research reproducibility guideline
• Project Closing
• Research Publication

---

Filter by tag Filter by tag aria-label="Filter by tag" .dmg .exe .pkg .zip Adobe Alfred App Store GUI Microsoft Office Slack Teams Zoom browser-extensions collaboration coordination decision-making linux local-machine macOS messaging package-manager password-manager productivity-tools research-team screen-capture source-code strategy terminal text-editor video-conferencing video-editor virtual-communication windows

• Must-have software
• Basic office software
• Various methods of software installation
• Collaboration & Communication
• Team communication tools
• Introduction to Slack

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .configure .jar .rpm .tar.gz API ASCII-art BeautifulSoup Bioconductor CLI CLI-login CLI-navigation CPU CSV CyVerse Cyberduck FileZilla GPU GUI GridFTP HPC-system HPC-tasks HTTP HTTPS IDE IDLE IJulia IP-address ImageMagic JOBID JSON LSF Makefile OOD OOD-login PBS PDF PNG PowerShell R RESTful SLURM SQL SSH TSV TXT VPN Vagrant WINscp WSL X11-forwarding XML access-point aggregate-data algorithm alias apptainer apt-list arithmetic artificial-intelligence ascii-image-converter ascii-python asciiview atlas-cluster authentication-MFA auto-completion awk backup bash batch batch-download big-data binary binary-search bioawk bioinformatics blast-in-parallel bubble-sort calc-average cat cd ceres-cluster cmake cmp code-editor comm command-history command-piping common-divisor comparing-files compiler computer-power conda container control-flow core count count-words cp create-container curl custom-software cut cut-characters data-aggregation data-archiving data-cleaning data-collection data-copy data-download data-exploration data-filtering data-move data-object data-online data-reshape data-security data-selection data-sharing data-splitting data-upload data-wrangling database dataset debugger dependencies development-environment diff disk-space download excel export-path factorial feeding-inputs file-compression file-decompression file-format file-operations file-size file-system firefox first-time-setup global-definitions globus gnuplot graphic-files graphics grep group-by head home-dir hpc-cluster iRODS iRODS-client iRODS-server identify-job-scheduler img2txt import in-browser inputs interactive-session interface interpreter java job-history job-management job-script job-submission join join-merge jp2a julia jupyter kernel less library linear-search linux local-machine logical-operator long-term-storage loop ls macOS machine-learning manage-order manual-guide mcedit memory merge-files-by-col mkdir modify-container module module-avail module-list module-load module-purge module-show more mount-folder multi-job mv nano node numerical-computing numpy od openpyxl operating-system outputs ownership package package-manager pandas parallel password-generator paste path performance-optimization perl permission-denied permissions pkg process-multiple-files processor project-dir prompt pseudocode pull-from-docker pull-from-singularity-hub pwd python python-shell qdel qhold qstat qsub qsub-depend queue raw-data read-write regex regular-expression remote-machine replace-pattern requests resource-allocation reverse-string rm root rsync salloc sbatch scalable scancel scientific-computing scontrol scp script-file search-pattern sed select-col select-row selenium shell-variables shortcuts sinfo singularity singularity-build singularity-exec softlink sort sort-lines source-code split-data spreadsheet squeue sshfs standard-error standard-output storage-quota sudo sum super-computer superuser swap-characters synchronize syntax syntax-highlighting tac tail terminal text-editor text-files tr ubuntu unix urllib use-multiple-cores variable vim virtual-env web-scraping web-server wget windows workdir workload-manager yum-list-all zipping-files

• Getting started with macOS
• Windows command-line environments
• Configuring your Linux system
• 03: Introduction to Command Line
• Terminal - an interface for command-line operations
• Introduction to UNIX Shell: configuration, variables, home dir
• Basic Commands: navigation, file creation & preview
• Command Line text files editors: nano, vim
• System info and access permissions
• Superuser command: sudo
• Getting started with UNIX + video + exercises
• Useful text manipulation programs
• GREP – simple search for regular expressions
• SED – replace pattern in stream text
• AWK – advanced text processing
• BIOAWK – biological data manipulation
• DIFF, COMM, CMP – comparing and collating two files with Unix
• UNIX Commands
• Shell & IDLE: Python code in a terminal or simple IDE
• Text editors: create Python code in terminal text files
• Basics of Algorithm Structure
• Introduction to Bash scripting
• Process multiple files
• Introduction to regular expression
• Julia setup: installation, environments and Jupyter integration
• Introduction to HPC infrastructure
• Secure Shell Connection (SSH)
• SSH shortcuts and password-less login
• Open On Demand (OOD) Connection
• Setting up your home directory for data analysis
• Example .bashrc file configuration
• Software Available on HPC
• Accessing pre-installed modules
• Accessing software via package manager
• Installing custom programs in user space
• Introduction to job scheduling
• SLURM: basics of workload manager
• Introduction to SLURM
• SLURM commands
• Creating SLURM job submission scripts
• Submitting dependency jobs using SLURM
• PBS: Portable Batch System
• PBS commands
• Creating PBS job submission scripts
• Submitting dependency jobs using PBS
• Introduction to GNU parallel
• Apptainer: the container system for secure HPC
• Singularity
• Creating containers using Singularity
• Modifying existing containers
• Singularity on your Mac via Vagrant
• 07: Data Acquisition and Wrangling
• Remote data access
• Remote data transfer
• Copying Data using Graphical Interface: Globus
• Copying Data via SSH using Command Line: scp, rsync
• File transfer using irods
• Remote data download
• Downloading Online Data using WGET
• Downloading online data using API
• Downloading online data using Python-based web scraping
• Remote data preview
• Viewing text files using UNIX commands
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Mounting remote folder on a local machine
• Data manipulation
• Manipulating text files with Python
• Read, write, split, select data
• Data wrangling: use ready-made apps
• Merge files by common column
• Aggregate data over slicing variations
• Split data or create data chunks

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .configure .dmg .exe .jar .pkg .rpm .tar.gz .zip ACCESS API ASCII-art App Store BeautifulSoup Bioconductor CLI CLI-login CPU CSV Cisco AnyConnect CyVerse Cyberduck FileZilla GPU GUI GitHub Globus GridFTP HPC-system HPC-tasks HTTP HTTPS ISU-HPC ImageMagic JOBID JSON LSF LSS-storage Makefile OOD OOD-login PBS PDF PNG R RESTful RFS SCINet SLURM SSH SVN TSV TXT VPN Vagrant WINscp X11-forwarding XML XSEDE access-point access-supercell alias apptainer apt-list artificial-intelligence ascii-image-converter ascii-python asciiview atlas-cluster authentication-MFA backup backups bash batch batch-download binary bioinformatics blast-in-parallel cat ceres-cluster clone-repo cmake compiler computer-power conda condo-cluster container core create-container curl custom-software data-archiving data-collection data-copy data-download data-exploration data-move data-online data-security data-sharing data-upload database dataset deadline debugger dependencies distributed-computing docker docker-pull docker-run download feeding-inputs file-compression file-decompression file-format firefox get-github-file get-github-folder git globus gnuplot goals graphic-files graphics head home-dir hosting-platform hpc-cluster iRODS iRODS-client iRODS-server identify-job-scheduler img2txt in-browser interactive-session interface java job-history job-management job-script job-submission jp2a julia juno-storage knowledge-retention kubernetes less library linux local-machine long-term-storage macOS machine-learning modify-container module module-avail module-list module-load module-purge module-show more mount-folder multi-job nextflow node nova-cluster numerical-computing objectives od package package-manager pandas parallel performance-optimization perl permissions productivity project-dir pull-from-docker pull-from-singularity-hub python qdel qhold qstat qsub qsub-depend queue raw-data remote-machine repository reproducibility requests resource-allocation rsync salloc sbatch scalable scancel scientific-computing scontrol scp selenium sinfo singularity singularity-build singularity-exec source-code squeue sshfs standards storage-quota strategy super-computer superuser svn-export synchronize tac tail terminal text-files timeline urllib use-multiple-cores virtual-env virtual-machine web-scraping web-server wget windows workdir workload-manager yum-list-all zipping-files

• Must-have software
• Various methods of software installation
• Introduction to HPC infrastructure
• ACCESS - an advanced computing and data resource program
• XSEDE supercell storage
• SCINet Scientific Computing: HPC, high-speed networking and training
• SCINet: Atlas computing cluster
• SCINet: Ceres computing cluster
• SCINet: Juno storage
• ISU HPC Network
• ISU HPC: Condo computing cluster
• ISU HPC: Nova computing cluster
• ISU HPC: LSS system
• Remote Access to HPC resources
• Virtual Private Network (VPN) Connection
• Secure Shell Connection (SSH)
• SSH shortcuts and password-less login
• Open On Demand (OOD) Connection
• Software Available on HPC
• Accessing pre-installed modules
• Accessing software via package manager
• Installing custom programs in user space
• Introduction to job scheduling
• SLURM: basics of workload manager
• Introduction to SLURM
• SLURM commands
• Creating SLURM job submission scripts
• Submitting dependency jobs using SLURM
• PBS: Portable Batch System
• PBS commands
• Creating PBS job submission scripts
• Submitting dependency jobs using PBS
• Introduction to GNU parallel
• Introduction to containers
• Apptainer: the container system for secure HPC
• Singularity
• Creating containers using Singularity
• Modifying existing containers
• Singularity on your Mac via Vagrant
• Docker - accelerated container application development
• Remote data access
• Remote data transfer
• Copying Data using Graphical Interface: Globus
• Copying Data via SSH using Command Line: scp, rsync
• File transfer using irods
• Remote data download
• Downloading Online Data using WGET
• Downloading online data using API
• Downloading online data using Python-based web scraping
• Downloading online repos using GIT: [GitHub, Bitbucket, SourceForge]
• Downloading a single folder or file from GitHub
• Remote data preview
• Viewing text files using UNIX commands
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Mounting remote folder on a local machine
• Enhancing productivity in research
• Reproducibility in research
• Research reproducibility guideline

---

Filter by tag Filter by tag aria-label="Filter by tag" CLI GUI Vagrant apptainer container create-container docker docker-pull docker-run hpc-cluster kubernetes local-machine macOS modify-container nextflow permissions pull-from-docker pull-from-singularity-hub remote-machine singularity singularity-build singularity-exec superuser terminal virtual-env virtual-machine workdir

• Introduction to containers
• Apptainer: the container system for secure HPC
• Singularity
• Creating containers using Singularity
• Modifying existing containers
• Singularity on your Mac via Vagrant
• Docker - accelerated container application development

---

Filter by tag Filter by tag aria-label="Filter by tag" API BeautifulSoup CLI GitHub HTTP HTTPS JSON OOD RESTful SSH SVN VPN XML access-point batch-download big-data clone-repo curl data-archiving data-collection data-download data-exploration data-online data-security data-sharing data-wrangling database download get-github-file get-github-folder git hosting-platform hpc-cluster in-browser pandas python raw-data remote-machine repository requests selenium svn-export terminal urllib web-scraping web-server wget

• 07: Data Acquisition and Wrangling
• Remote data access
• Remote data download
• Downloading Online Data using WGET
• Downloading online data using API
• Downloading online data using Python-based web scraping
• Downloading online repos using GIT: [GitHub, Bitbucket, SourceForge]
• Downloading a single folder or file from GitHub

---

Filter by tag Filter by tag aria-label="Filter by tag" CARE DMP FAIR OneNote SciNote Slack TRUST artificial-intelligence backup backups code-docs collaboration count-files data-archiving data-collection data-docs data-lifecycle data-security data-sharing deadline docs-generator eLabFTW ethics file-list file-size goals jupyter knowledge-retention markdown note-taking notebook objectives open-access open-data open-methods open-review open-science open-source open-standards productivity publication raw-data reference-manager reproducibility source-code standards strategy timeline workdir

• Data Management
• Open Science policy
• FAIR principles
• CARE principles
• TRUST principles
• Data Management Plan
• Documentation improvement tools
• A Practical guide to managing research documentation
• Tools for research documentation
• Quality Assurance
• Monitoring & Evaluation
• Enhancing productivity in research
• Reproducibility in research
• Research reproducibility guideline
• Project Closing
• Research Publication

---

Filter by tag Filter by tag aria-label="Filter by tag" .xlsx ANOVA-test Apple Numbers CSV Google Sheets HTML IDE JSON LibreOffice Calc Pearson-correlation R SQL T-test VBA XML add-remove-data aggregate data aggregate-data algorithm arithmetic array big-data binary box-plot centroid chart clean-data clustering code-editor colorscale compare-data conda constant data-aggregation data-archiving data-cleaning data-download data-entry data-exploration data-file data-filtering data-formatting data-indexing data-object data-reshape data-security data-selection data-separator data-sharing data-slicing data-splitting data-wrangling data.table dataframe dataset dependencies development-environment dictionary distributed-computing dplyr error-handling excel explore-data f-string file-format file-line-by-line filter-data formula function generate-random-sample ggplot ggplot2 group-by handling-errors hierarchical-clustering import in-browser inputs join-merge jupyter k-means-clustering kernel library linear-regression local-machine macOS macro markdown math matrix merge-files-by-col mirror-plot module multiple-files-to-worksheet notebook numerical-computing numpy object open-close openpyxl operator opertor outputs package package-manager pandas plotly python raw-data read-write scatter-plot scientific-computing scipy select-col select-row series split-data spreadsheet statistics summarize text-files tidyverse variable vector virtual-env windows workdir worksheet-index worksheet-to-files

• Jupyter Lab: create an interactive Python notebook
• Open-Close & Read-Write of data files
• JSON module - encoding & decoding JSON data
• Math module - various mathematical functions
• Pandas library - data structure manipulation tool
• NumPy library - multi-dimensional arrays parser
• SciPy library - algorithms for scientific computing
• Introduction to R programming
• Base R - core functionality for statistical computing
• Base R Graphics - traditional statistical graphing
• ggplot2 - customizable graphs and charts
• dplyr - data manipulation and transformation
• tidyverse - advanced data manipulation, exploration and visualization
• data.table - aggregation and manipulation of large data sets
• 07: Data Acquisition and Wrangling
• Data manipulation
• Manipulating Excel data sheets
• Create worksheet from multiple text files
• Export multiple worksheets as separate text files
• Create index for all worksheets
• Merge two spreadsheets using a common column
• Manipulating text files with Python
• Read, write, split, select data
• Data wrangling: use ready-made apps
• Merge files by common column
• Aggregate data over slicing variations
• Split data or create data chunks

---

Filter by tag Filter by tag aria-label="Filter by tag" ASCII-art Apple Numbers CSV Google Sheets ImageMagic LibreOffice Calc OOD PDF PNG RESTful SSH TSV TXT VPN X11-forwarding access-point ascii-image-converter ascii-python asciiview bash binary cat data-cleaning data-download data-entry data-exploration data-formatting excel file-format firefox gnuplot graphic-files graphics head hpc-cluster img2txt in-browser jp2a less local-machine more mount-folder od remote-machine spreadsheet sshfs tac tail terminal text-files

• Remote data access
• Remote data preview
• Viewing text files using UNIX commands
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Mounting remote folder on a local machine
• Manipulating Excel data sheets

---

Filter by tag Filter by tag aria-label="Filter by tag" artificial-intelligence big-data binary bioinformatics computational data-archiving data-download data-exploration data-security data-sharing data-states data-wrangling digital-data distributed-computing geospatial information interactive-graphing knowledge machine-learning scientific structured-data unstructured-data

• 01: Introduction to Data Science
• Data Science Principles
• Applications of Computational Science
• Computational Biology
• Geospatial Analytics
• Machine Learning
• 07: Data Acquisition and Wrangling

---

Filter by tag Filter by tag aria-label="Filter by tag" CARE CLI-login DMP FAIR Globus HPC-system HPC-tasks ISU-HPC LSS-storage SCINet TRUST access-point authentication-MFA backup data-archiving data-copy data-move data-security data-sharing ethics juno-storage long-term-storage raw-data rsync scp standards storage-quota

• SCINet: Juno storage
• ISU HPC: LSS system
• Data Management Plan

---

Filter by tag Filter by tag aria-label="Filter by tag" ACCESS CLI CLI-login CyVerse Cyberduck FileZilla GUI Globus GridFTP HPC-system HPC-tasks ISU-HPC LSS-storage OOD OOD-login R RESTful SCINet SSH VPN WINscp XSEDE access-point access-supercell alias atlas-cluster authentication-MFA backup bash ceres-cluster compiler computer-power condo-cluster custom-software data-archiving data-copy data-download data-move data-security data-sharing data-upload dataset debugger distributed-computing file-compression globus hpc-cluster iRODS iRODS-client iRODS-server in-browser interface job-management job-script julia juno-storage library long-term-storage module nova-cluster package package-manager permissions python remote-machine rsync scientific-computing scp storage-quota super-computer synchronize terminal workdir

• XSEDE supercell storage
• SCINet: Atlas computing cluster
• SCINet: Ceres computing cluster
• SCINet: Juno storage
• ISU HPC: Condo computing cluster
• ISU HPC: Nova computing cluster
• ISU HPC: LSS system
• Software Available on HPC
• Remote data access
• Remote data transfer
• Copying Data using Graphical Interface: Globus
• Copying Data via SSH using Command Line: scp, rsync
• File transfer using irods

---

Filter by tag Filter by tag aria-label="Filter by tag" .xlsx AI ANOVA-test API ASCII-art Adobe Express Adobe Illustrator Adobe Photoshop Affinity Designer Affinity Photo BioRender CLI CSV Canva CorelDRAW EPS GIMP Google Drawings HTML HTTP HTTPS IDE IJulia ImageMagic Infogram Inkscape JPEG JSON Mind the Graph OOD PDF PNG Pearson-correlation Pixlr PyCall R RCall SQL SVG Sketch SmartDraw T-test TIFF TSV TXT Visme X11-forwarding XML access-point add-remove-data aggregate data animation arithmetic array artificial-intelligence ascii-image-converter ascii-python asciiview audio bash big-data binary bioawk bioinformatics box-plot break cat centroid class clean-data clustering constant continue control-flow data-exploration data-file data-formatting data-indexing data-separator data-slicing data-states dataframe dataset dependencies design development-environment dictionary digital-data distributed-computing e-signature error-handling explore-data f-string file-format file-line-by-line filter-data firefox function generate-random-sample ggplot gnuplot graphic-files graphics handling-errors head hierarchical-clustering hpc-cluster if-else img2txt import in-browser infographic information interactive-graphing jp2a julia jupyter k-means-clustering kernel knowledge less linear-regression loop macros manual-guide math matrix metaprogramming mirror-plot module more mount-folder multiple-dispatch numerical-computing numpy object od open-close operator opertor package-manager pandas pixel pkg python raster read-write scalable scientific scientific-computing scipy series sshfs statistics structured-data syntax tac tail terminal text-files try-except unix unstructured-data variable vector video virtual-env workdir

• Data Science Principles
• BIOAWK – biological data manipulation
• Introduction to Python programming
• Open-Close & Read-Write of data files
• JSON module - encoding & decoding JSON data
• Math module - various mathematical functions
• Pandas library - data structure manipulation tool
• NumPy library - multi-dimensional arrays parser
• SciPy library - algorithms for scientific computing
• Introduction to R programming
• Introduction to Julia programming
• Julia setup: installation, environments and Jupyter integration
• Downloading online data using API
• Remote data preview
• Viewing text files using UNIX commands
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Raster graphics tools
• Vector graphics tools
• Adobe creative cloud
• Template-based web tools

---

Filter by tag Filter by tag aria-label="Filter by tag" PowerShell Python R WSL bash file-management local-machine operating-system windows

• Automated batch file operations on Windows

---

Filter by tag Filter by tag aria-label="Filter by tag" .dmg .exe .pkg .zip App Store Atom BitBucket CLI CodeAcademy GUI GitHub IDE IDLE IJulia Mercurial Midnight Commander OOD PyPI PythonAnywhere R RStudio SVN VPN VSC anaconda arithmetic binary calc-average code-editor code-sharing code-storage colab command commit compiler conda count-words data-storage debugger dependencies development-environment docker dplyr file-manager gcc ggplot git github homebrew hosting-platform hpc-cluster import in-browser interface interpreter java julia jupyter kernel library linux local-machine local-repo macOS manage-conflicts markdown math matplotlip mcedit module my-binder nano nextflow notebook numpy openpyxl operating-system package package-manager pandas password-generator perl pkg plotly pull-updates push-changes python python-console python-shell remote-repo repository scatter-plot scipy script-file seaborn source-code standards subversion terminal text-editor tidyverse variable venv vim virtual-env windows workdir

• Must-have software
• Basic developer tools
• Basic developer libraries
• Various methods of software installation
• Installations on MacBook Pro
• Installations on Windows
• Installations on Linux
• 04: Development Environment
• Integrated & Interactive Development Environment (IDE)
• Visual Studio Code: multi-language integrated DE (VSC)
• Jupyter: interactive web-based multi-kernel DE
• Getting started with JupyterLab on a local machine
• Getting started with Jupyter Notebook on HPC systems
• Sharing Jupyter-based reproducible pipline via MyBinder
• Python programming environment(s)
• Online Console: simple Python code in a browser
• Online Notebook: interactive Python on Try-jupyter and Colab
• Local Python setup on your computing machine
• Shell & IDLE: Python code in a terminal or simple IDE
• Text editors: create Python code in terminal text files
• Jupyter Lab: create an interactive Python notebook
• PyCharm: IDE for professional Python developers
• R programming environment(s)
• RStudio: integrated environment for R programming
• Setting up RStudio
• Julia setup: installation, environments and Jupyter integration
• Storage & Version Control
• GIT - a distributed version control system
• GIT Commands
• Online hosting platforms for GIT repositories
• Introduction to GitHub
• GitHub - getting started
• GitHub - getting started (class exercise)
• Introduction to BitBucket

---

Filter by tag Filter by tag aria-label="Filter by tag" TRUST standards

• TRUST principles

---

Filter by tag Filter by tag aria-label="Filter by tag" BitBucket CARE CLI CLI-login DMP FAIR GUI GitHub Globus HPC-system HPC-tasks IDE ISU-HPC LSS-storage Mercurial OOD OOD-login OneNote R SCINet SVN SciNote Slack TRUST VSC access-point agile artificial-intelligence atlas-cluster authentication-MFA backup backups bash binary ceres-cluster code-archiving code-docs code-editor code-lifecycle code-release code-sharing code-storage code-testing collaboration command comments commit computer-power condo-cluster config count-files data-archiving data-collection data-copy data-docs data-lifecycle data-move data-security data-sharing data-storage deadline debugger decision-making distributed-computing docs-generator docstring eLabFTW ethics file-list file-size git github goals hosting-platform hpc-cluster in-browser interface job-script juno-storage jupyter knowledge-retention local-machine local-repo long-term-storage manage-conflicts markdown messaging my-binder note-taking notebook nova-cluster objectives productivity publication pull-updates push-changes python raw-data readme reference-manager remote-repo repository reproducibility research-team rsync scientific scientific-computing scp source-code standards storage-quota strategy subversion super-computer syntax terminal timeline workdir

• Must-have software
• Getting started with JupyterLab on a local machine
• Getting started with Jupyter Notebook on HPC systems
• Sharing Jupyter-based reproducible pipline via MyBinder
• SCINet Scientific Computing: HPC, high-speed networking and training
• SCINet: Atlas computing cluster
• SCINet: Ceres computing cluster
• SCINet: Juno storage
• ISU HPC Network
• ISU HPC: Condo computing cluster
• ISU HPC: Nova computing cluster
• ISU HPC: LSS system
• Overview of essential tools for modern research
• Introduction to Slack
• Data Management
• Data Management Plan
• Code Development & Management
• Storage & Version Control
• GIT - a distributed version control system
• GIT Commands
• Online hosting platforms for GIT repositories
• Introduction to GitHub
• GitHub - getting started
• GitHub - getting started (class exercise)
• Introduction to BitBucket
• Documentation improvement tools
• A Practical guide to managing research documentation
• Tools for research documentation
• Tools for code documentation
• Introduction to Markdown
• Quality Assurance
• Monitoring & Evaluation
• Enhancing productivity in research
• Reproducibility in research
• Research reproducibility guideline
• Project Closing
• Research Publication

---

Filter by tag Filter by tag aria-label="Filter by tag" .dmg .exe .pkg .zip 2D-plot 3D-plot AI Adobe Adobe Express Adobe Illustrator Adobe Photoshop Affinity Designer Affinity Photo Alfred App Store BioRender Canva ComplexHeatmap CorelDRAW EPS GIMP GUI Google Charts Google Drawings Heatplus Highcharts IDE Infogram Inkscape JPEG Microsoft Office Mind the Graph PDF PNG Piktochart Pixlr R RStudio SVG Sketch SmartDraw TIFF Tableau Public Visme animation audio barplot box-plot browser-extensions chart charts clustergram-plot colorscale conda dash dataset dendrogram-plot dependencies design development-environment e-signature excel filled-curves ggplot gnuplot graph-layout graphics heatmap heatmap-plot histogram infographic interactive-graphing jupyter linux local-machine macOS machine-learning mathplotlib notebook package-manager password-manager pixel plot-data-from-file plot-math-formula plotly productivity-tools python raster raw-data scalable scatter-plot scatterplot scientific screen-capture source-code syntax terminal text-editor variable vector video video-editor virtual-communication virtual-env volcano-plot widgets windows workdir

• Must-have software
• Basic office software
• Various methods of software installation
• 08: Data Visualization
• Introduction to scientific graphic design
• Raster graphics tools
• Vector graphics tools
• Adobe creative cloud
• Template-based web tools
• Introduction to scientific graphing
• Gnuplot: creating plots in the UNIX Shell
• Gnuplot: variables, loops, conditionals
• Gnuplot: filled curves
• Plotly-Dash: interactive plotting with Python
• Introduction to Plotly
• Introduction to Dash
• Plotly graphing - interactive examples in the JupyterLab
• Creating XY scatter plot
• Creating 1D volcano plot
• Creating heatmap
• Creating dendrogram
• Creating clustergram
• RStudio – data processing & plotting with R
• Creating boxplots in R
• Creating heatmaps in R
• Creating heatmaps in R using ComplexHeatmap

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .configure .jar .rpm .tar.gz ACCESS ASCII-art Bioconductor CLI CLI-login CPU CSV Cisco AnyConnect Cyberduck FileZilla GPU GUI Globus GridFTP HPC-system HPC-tasks IDE IJulia ISU-HPC ImageMagic JOBID LSF LSS-storage Makefile OOD OOD-login PBS PDF PNG R RESTful RFS RStudio SCINet SLURM SSH TSV TXT VPN Vagrant WINscp X11-forwarding XSEDE access-point access-supercell alias apptainer apt-list artificial-intelligence ascii-image-converter ascii-python asciiview atlas-cluster authentication-MFA backup bash batch big-data binary bioinformatics blast-in-parallel cat ceres-cluster cmake code-editor compiler computer-power conda condo-cluster container core create-container custom-software data-archiving data-copy data-download data-exploration data-move data-security data-sharing data-upload data-wrangling debugger dependencies development-environment distributed-computing docker export-path feeding-inputs file-compression file-decompression file-format file-system firefox first-time-setup global-definitions globus gnuplot graphic-files graphics head home-dir hpc-cluster identify-job-scheduler img2txt in-browser interactive-session interface java job-history job-management job-script job-submission jp2a julia juno-storage jupyter kernel kubernetes less library local-machine long-term-storage macOS machine-learning markdown modify-container module module-avail module-list module-load module-purge module-show more mount-folder multi-job nextflow node notebook nova-cluster numerical-computing od package package-manager parallel performance-optimization perl pkg project-dir pull-from-docker pull-from-singularity-hub python qdel qhold qstat qsub qsub-depend queue raw-data remote-machine resource-allocation rsync salloc sbatch scalable scancel scientific-computing scontrol scp script-file sinfo singularity singularity-build singularity-exec softlink source-code squeue sshfs storage-quota super-computer tac tail terminal text-files use-multiple-cores virtual-env virtual-machine windows workdir workload-manager yum-list-all zipping-files

• Jupyter: interactive web-based multi-kernel DE
• Getting started with Jupyter Notebook on HPC systems
• RStudio: integrated environment for R programming
• Setting up RStudio
• Julia setup: installation, environments and Jupyter integration
• 06: High-Performance Computing (HPC)
• Introduction to HPC infrastructure
• ACCESS - an advanced computing and data resource program
• XSEDE supercell storage
• SCINet Scientific Computing: HPC, high-speed networking and training
• SCINet: Atlas computing cluster
• SCINet: Ceres computing cluster
• SCINet: Juno storage
• ISU HPC Network
• ISU HPC: Condo computing cluster
• ISU HPC: Nova computing cluster
• ISU HPC: LSS system
• Remote Access to HPC resources
• Virtual Private Network (VPN) Connection
• Secure Shell Connection (SSH)
• SSH shortcuts and password-less login
• Open On Demand (OOD) Connection
• Setting up your home directory for data analysis
• Example .bashrc file configuration
• Software Available on HPC
• Accessing pre-installed modules
• Accessing software via package manager
• Installing custom programs in user space
• Introduction to job scheduling
• SLURM: basics of workload manager
• Introduction to SLURM
• SLURM commands
• Creating SLURM job submission scripts
• Submitting dependency jobs using SLURM
• PBS: Portable Batch System
• PBS commands
• Creating PBS job submission scripts
• Submitting dependency jobs using PBS
• Introduction to GNU parallel
• Introduction to containers
• Apptainer: the container system for secure HPC
• Singularity
• Creating containers using Singularity
• Modifying existing containers
• Singularity on your Mac via Vagrant
• 07: Data Acquisition and Wrangling
• Remote data access
• Remote data transfer
• Copying Data using Graphical Interface: Globus
• Copying Data via SSH using Command Line: scp, rsync
• Remote data preview
• Viewing text files using UNIX commands
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Mounting remote folder on a local machine

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc CLI-login GUI HPC-system HPC-tasks ISU-HPC JOBID LSF OOD PBS R SLURM access-point alias authentication-MFA bash compiler computer-power condo-cluster custom-software debugger dependencies file-compression hpc-cluster identify-job-scheduler in-browser interactive-session interface job-history job-management job-script job-submission julia library machine-learning module module-avail module-list module-load module-purge module-show multi-job nova-cluster numerical-computing package package-manager performance-optimization python qdel qhold qstat qsub qsub-depend queue remote-machine resource-allocation salloc sbatch scancel scientific-computing scontrol sinfo squeue super-computer terminal workdir workload-manager

• ISU HPC: Condo computing cluster
• ISU HPC: Nova computing cluster
• Software Available on HPC
• Accessing pre-installed modules
• Introduction to job scheduling
• SLURM: basics of workload manager
• Introduction to SLURM
• SLURM commands
• Creating SLURM job submission scripts
• Submitting dependency jobs using SLURM
• PBS: Portable Batch System
• PBS commands
• Creating PBS job submission scripts
• Submitting dependency jobs using PBS

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .configure .jar .rpm .tar.gz .xlsx ANOVA-test BeautifulSoup Bioconductor CPU CSV ComplexHeatmap GUI HTML Heatplus IDE JSON Makefile OOD Pearson-correlation PyPI R RStudio SQL T-test Vagrant add-remove-data aggregate data aggregate-data algorithm alias anaconda apptainer apt-list arithmetic array artificial-intelligence barplot bash batch-download binary bioinformatics blast-in-parallel box-plot break centroid chart charts class clean-data clustergram-plot clustering cmake code-editor colab colorscale compare-data compiler computer-power conda constant container continue control-flow create-container custom-software dash data-aggregation data-cleaning data-download data-exploration data-file data-filtering data-formatting data-indexing data-object data-reshape data-selection data-slicing data-splitting data.table dataframe dataset debugger dendrogram-plot dependencies development-environment dictionary distributed-computing docker dplyr error-handling explore-data feeding-inputs file-compression file-decompression file-format filter-data function generate-random-sample ggplot ggplot2 github group-by heatmap heatmap-plot hierarchical-clustering histogram home-dir hpc-cluster if-else import in-browser inputs interactive-graphing interface java job-management join-merge julia jupyter k-means-clustering kernel library linear-regression local-machine loop macOS machine-learning markdown math matplotlip matrix merge-files-by-col mirror-plot modify-container module module-avail module-list module-load module-purge module-show notebook numerical-computing numpy object openpyxl operator opertor outputs package package-manager pandas parallel perl plotly project-dir pull-from-docker pull-from-singularity-hub python raw-data read-write remote-machine requests scalable scatter-plot scatterplot scientific-computing scipy seaborn select-col select-row selenium series singularity singularity-build singularity-exec source-code split-data spreadsheet statistics summarize syntax terminal text-files tidyverse try-except urllib use-multiple-cores variable vector venv virtual-env volcano-plot web-scraping widgets workdir yum-list-all zipping-files

• Basic developer libraries
• Online Notebook: interactive Python on Try-jupyter and Colab
• Local Python setup on your computing machine
• Jupyter Lab: create an interactive Python notebook
• Setting up RStudio
• Introduction to Python programming
• JSON module - encoding & decoding JSON data
• Math module - various mathematical functions
• Pandas library - data structure manipulation tool
• NumPy library - multi-dimensional arrays parser
• SciPy library - algorithms for scientific computing
• Introduction to R programming
• Base R - core functionality for statistical computing
• Base R Graphics - traditional statistical graphing
• ggplot2 - customizable graphs and charts
• dplyr - data manipulation and transformation
• tidyverse - advanced data manipulation, exploration and visualization
• data.table - aggregation and manipulation of large data sets
• Software Available on HPC
• Accessing pre-installed modules
• Accessing software via package manager
• Installing custom programs in user space
• Introduction to GNU parallel
• Apptainer: the container system for secure HPC
• Singularity
• Creating containers using Singularity
• Modifying existing containers
• Singularity on your Mac via Vagrant
• Downloading online data using Python-based web scraping
• Manipulating text files with Python
• Read, write, split, select data
• Data wrangling: use ready-made apps
• Merge files by common column
• Aggregate data over slicing variations
• Split data or create data chunks
• Plotly-Dash: interactive plotting with Python
• Introduction to Plotly
• Introduction to Dash
• Plotly graphing - interactive examples in the JupyterLab
• Creating XY scatter plot
• Creating 1D volcano plot
• Creating heatmap
• Creating dendrogram
• Creating clustergram
• RStudio – data processing & plotting with R
• Creating boxplots in R
• Creating heatmaps in R
• Creating heatmaps in R using ComplexHeatmap

---

Filter by tag Filter by tag aria-label="Filter by tag" .dmg .exe .pkg .zip Adobe Alfred App Store GUI Microsoft Office browser-extensions linux local-machine macOS package-manager password-manager productivity-tools screen-capture source-code terminal text-editor video-editor virtual-communication windows

• Must-have software
• Basic office software
• Various methods of software installation

---

Filter by tag Filter by tag aria-label="Filter by tag" CPU GPU HPC-system HPC-tasks SLURM SSH artificial-intelligence batch bioinformatics blast-in-parallel computer-power core feeding-inputs hpc-cluster job-script module module-load node parallel queue raw-data scalable super-computer terminal use-multiple-cores workdir zipping-files

• Introduction to HPC infrastructure
• Introduction to GNU parallel

---

Filter by tag Filter by tag aria-label="Filter by tag" 2D-plot 3D-plot Apple Numbers ComplexHeatmap GUI Google Charts Google Sheets Heatplus Highcharts IDE LibreOffice Calc OOD R RStudio Tableau Public barplot bash box-plot chart charts clustergram-plot code-editor colab colorscale compiler conda dash data-cleaning data-entry data-formatting dataframe dataset debugger dendrogram-plot dependencies development-environment excel filled-curves ggplot ggplot2 gnuplot graph-layout heatmap heatmap-plot histogram hpc-cluster import in-browser interactive-graphing julia jupyter kernel library linux local-machine macOS machine-learning markdown mathplotlib matplotlip matrix mirror-plot module module-avail module-list module-load module-purge module-show notebook numerical-computing object operator package package-manager plot-data-from-file plot-math-formula plotly python raw-data read-write scatter-plot scatterplot scientific scientific-computing script-file seaborn spreadsheet statistics syntax terminal variable vector virtual-env volcano-plot widgets windows workdir

• Jupyter: interactive web-based multi-kernel DE
• Online Notebook: interactive Python on Try-jupyter and Colab
• Jupyter Lab: create an interactive Python notebook
• RStudio: integrated environment for R programming
• Setting up RStudio
• Introduction to R programming
• Base R Graphics - traditional statistical graphing
• ggplot2 - customizable graphs and charts
• Accessing pre-installed modules
• Manipulating Excel data sheets
• 08: Data Visualization
• Introduction to scientific graphing
• Gnuplot: creating plots in the UNIX Shell
• Gnuplot: variables, loops, conditionals
• Gnuplot: filled curves
• Plotly-Dash: interactive plotting with Python
• Introduction to Plotly
• Introduction to Dash
• Plotly graphing - interactive examples in the JupyterLab
• Creating XY scatter plot
• Creating 1D volcano plot
• Creating heatmap
• Creating dendrogram
• Creating clustergram
• RStudio – data processing & plotting with R
• Creating boxplots in R
• Creating heatmaps in R
• Creating heatmaps in R using ComplexHeatmap

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .configure .jar .rpm .tar.gz .xlsx ANOVA-test BeautifulSoup Bioconductor CSV CodeAcademy ComplexHeatmap GUI Google Charts HTML Heatplus Highcharts IDE IDLE IJulia JSON Makefile OOD Pearson-correlation PyCall PyPI PythonAnywhere R RCall RStudio SQL T-test Tableau Public VSC XML add-remove-data aggregate data aggregate-data algorithm alias anaconda apt-list arithmetic array artificial-intelligence barplot bash batch-download binary binary-search box-plot break bubble-sort calc-average centroid chart charts class clean-data clustergram-plot clustering cmake code-editor code-sharing colab colorscale common-divisor compare-data compiler conda constant continue control-flow count-words custom-software dash data-aggregation data-cleaning data-download data-exploration data-file data-filtering data-formatting data-indexing data-object data-reshape data-selection data-separator data-slicing data-splitting data.table dataframe dataset debugger dendrogram-plot dependencies development-environment dictionary distributed-computing docker dplyr error-handling excel explore-data f-string factorial file-compression file-decompression file-format file-line-by-line filter-data function generate-random-sample ggplot ggplot2 github gnuplot group-by handling-errors heatmap heatmap-plot hierarchical-clustering histogram home-dir hpc-cluster if-else import in-browser inputs interactive-graphing interface interpreter java job-management join-merge julia jupyter k-means-clustering kernel library linear-regression linear-search local-machine loop machine-learning macros markdown math mathplotlib matplotlip matrix mcedit merge-files-by-col metaprogramming mirror-plot module module-avail module-list module-load module-purge module-show multiple-dispatch my-binder nano notebook numerical-computing numpy object open-close openpyxl operator opertor outputs package package-manager pandas password-generator perl pkg plotly project-dir pseudocode python python-console python-shell raw-data read-write remote-machine reproducibility requests reverse-string scatter-plot scatterplot scientific scientific-computing scipy script-file seaborn select-col select-row selenium series source-code split-data spreadsheet statistics sum summarize syntax terminal text-editor text-files tidyverse try-except urllib variable vector venv vim virtual-env volcano-plot web-scraping widgets workdir yum-list-all

• Must-have software
• Basic developer libraries
• 04: Development Environment
• Visual Studio Code: multi-language integrated DE (VSC)
• Jupyter: interactive web-based multi-kernel DE
• Getting started with JupyterLab on a local machine
• Getting started with Jupyter Notebook on HPC systems
• Sharing Jupyter-based reproducible pipline via MyBinder
• Python programming environment(s)
• Online Console: simple Python code in a browser
• Online Notebook: interactive Python on Try-jupyter and Colab
• Local Python setup on your computing machine
• Shell & IDLE: Python code in a terminal or simple IDE
• Text editors: create Python code in terminal text files
• Jupyter Lab: create an interactive Python notebook
• PyCharm: IDE for professional Python developers
• R programming environment(s)
• RStudio: integrated environment for R programming
• Setting up RStudio
• 05: Introduction to Programming
• Basics of Algorithm Structure
• Introduction to Python programming
• Open-Close & Read-Write of data files
• JSON module - encoding & decoding JSON data
• Math module - various mathematical functions
• Pandas library - data structure manipulation tool
• NumPy library - multi-dimensional arrays parser
• SciPy library - algorithms for scientific computing
• Introduction to R programming
• Base R - core functionality for statistical computing
• Base R Graphics - traditional statistical graphing
• ggplot2 - customizable graphs and charts
• dplyr - data manipulation and transformation
• tidyverse - advanced data manipulation, exploration and visualization
• data.table - aggregation and manipulation of large data sets
• Introduction to Julia programming
• Julia setup: installation, environments and Jupyter integration
• Software Available on HPC
• Accessing pre-installed modules
• Accessing software via package manager
• Installing custom programs in user space
• Downloading online data using Python-based web scraping
• Data manipulation
• Manipulating text files with Python
• Read, write, split, select data
• Data wrangling: use ready-made apps
• Merge files by common column
• Aggregate data over slicing variations
• Split data or create data chunks
• Introduction to scientific graphing
• Plotly-Dash: interactive plotting with Python
• Introduction to Plotly
• Introduction to Dash
• Plotly graphing - interactive examples in the JupyterLab
• Creating XY scatter plot
• Creating 1D volcano plot
• Creating heatmap
• Creating dendrogram
• Creating clustergram
• RStudio – data processing & plotting with R
• Creating boxplots in R
• Creating heatmaps in R
• Creating heatmaps in R using ComplexHeatmap

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Filter by tag Filter by tag aria-label="Filter by tag" BitBucket CARE CLI DMP FAIR GUI GitHub Mercurial OneNote R SVN SciNote Slack TRUST Teams VSC Zoom agile artificial-intelligence backup backups bash binary code-archiving code-docs code-lifecycle code-release code-sharing code-storage code-testing collaboration command comments commit config coordination count-files data-archiving data-collection data-docs data-lifecycle data-security data-sharing data-storage deadline decision-making docs-generator docstring eLabFTW ethics file-list file-size framework git goals hosting-platform jupyter knowledge-retention local-repo manage-conflicts markdown messaging note-taking notebook objectives open-access open-data open-methods open-review open-science open-source open-standards planning productivity project-design publication pull-updates push-changes python raw-data readme reference-manager remote-repo repository reproducibility research-team resource-allocation resource-types risk-management risk-mitigation scientific source-code standards strategy subversion syntax timeline video-conferencing virtual-communication workdir

• Must-have software
• 09: Project Management
• Introduction to Project Management
• Overview of essential tools for modern research
• Project strategy and risk management
• Project Design vs Project Framework
• Collaboration & Communication
• Team communication tools
• Introduction to Slack
• Resource Management
• Data Management
• Open Science policy
• FAIR principles
• CARE principles
• TRUST principles
• Data Management Plan
• Code Development & Management
• Storage & Version Control
• GIT - a distributed version control system
• GIT Commands
• Online hosting platforms for GIT repositories
• Introduction to GitHub
• GitHub - getting started
• GitHub - getting started (class exercise)
• Introduction to BitBucket
• Documentation improvement tools
• A Practical guide to managing research documentation
• Tools for research documentation
• Tools for code documentation
• Introduction to Markdown
• Quality Assurance
• Monitoring & Evaluation
• Enhancing productivity in research
• Reproducibility in research
• Research reproducibility guideline
• Project Closing
• Research Publication

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Filter by tag Filter by tag aria-label="Filter by tag" API ASCII-art BeautifulSoup CLI CLI-login CSV Cisco AnyConnect CyVerse GUI GitHub Globus HPC-system HPC-tasks HTTP HTTPS ISU-HPC ImageMagic JSON LSS-storage OOD OOD-login PDF PNG R RESTful RFS SCINet SSH SVN TSV TXT VPN X11-forwarding XML access-point alias ascii-image-converter ascii-python asciiview atlas-cluster authentication-MFA backup bash batch-download big-data binary cat ceres-cluster clone-repo compiler computer-power condo-cluster curl custom-software data-archiving data-collection data-copy data-download data-exploration data-move data-online data-security data-sharing data-wrangling database dataset debugger distributed-computing download file-compression file-format firefox get-github-file get-github-folder git gnuplot graphic-files graphics head hosting-platform hpc-cluster iRODS iRODS-client iRODS-server img2txt in-browser interface job-management job-script jp2a julia juno-storage less library local-machine long-term-storage macOS module more mount-folder nova-cluster od package package-manager pandas permissions python raw-data remote-machine repository requests rsync scientific-computing scp selenium sshfs storage-quota super-computer svn-export synchronize tac tail terminal text-files urllib web-scraping web-server wget windows workdir

• Must-have software
• SCINet: Atlas computing cluster
• SCINet: Ceres computing cluster
• SCINet: Juno storage
• ISU HPC: Condo computing cluster
• ISU HPC: Nova computing cluster
• ISU HPC: LSS system
• Remote Access to HPC resources
• Virtual Private Network (VPN) Connection
• Secure Shell Connection (SSH)
• SSH shortcuts and password-less login
• Open On Demand (OOD) Connection
• Software Available on HPC
• 07: Data Acquisition and Wrangling
• Remote data access
• File transfer using irods
• Remote data download
• Downloading Online Data using WGET
• Downloading online data using API
• Downloading online data using Python-based web scraping
• Downloading online repos using GIT: [GitHub, Bitbucket, SourceForge]
• Downloading a single folder or file from GitHub
• Remote data preview
• Viewing text files using UNIX commands
• Viewing PDF and PNG files using X11 SSH connection
• Viewing graphics in a terminal as the text-based ASCII art
• Mounting remote folder on a local machine

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Filter by tag Filter by tag aria-label="Filter by tag" .bashrc API BeautifulSoup BitBucket CARE CLI CyVerse DMP FAIR GUI GitHub HTTP HTTPS JSON Mercurial OneNote R SVN SciNote Slack TRUST VSC XML access-point alias artificial-intelligence backup bash batch-download binary clone-repo code-archiving code-docs code-lifecycle code-release code-sharing code-storage code-testing collaboration command comments commit config count-files curl data-archiving data-collection data-docs data-download data-exploration data-lifecycle data-online data-security data-sharing data-storage database dataset docs-generator docstring download eLabFTW ethics export-path file-list file-size file-system first-time-setup get-github-file get-github-folder git global-definitions home-dir hosting-platform hpc-cluster iRODS iRODS-client iRODS-server jupyter knowledge-retention local-repo manage-conflicts markdown module note-taking notebook open-access open-data open-methods open-review open-science open-source open-standards pandas permissions productivity project-dir pull-updates push-changes python raw-data readme reference-manager remote-machine remote-repo repository reproducibility requests resource-allocation resource-types selenium singularity softlink source-code standards storage-quota subversion svn-export synchronize syntax terminal urllib web-scraping web-server wget workdir

• Setting up your home directory for data analysis
• Example .bashrc file configuration
• File transfer using irods
• Remote data download
• Downloading Online Data using WGET
• Downloading online data using API
• Downloading online data using Python-based web scraping
• Downloading online repos using GIT: [GitHub, Bitbucket, SourceForge]
• Downloading a single folder or file from GitHub
• Resource Management
• Data Management
• Open Science policy
• FAIR principles
• CARE principles
• TRUST principles
• Data Management Plan
• Code Development & Management
• Storage & Version Control
• GIT - a distributed version control system
• GIT Commands
• Online hosting platforms for GIT repositories
• Introduction to GitHub
• GitHub - getting started
• GitHub - getting started (class exercise)
• Introduction to BitBucket
• Documentation improvement tools
• A Practical guide to managing research documentation
• Tools for research documentation
• Tools for code documentation
• Introduction to Markdown

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Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .dmg .exe .pkg .zip App Store Atom CLI GUI IDE IP-address PowerShell Python R RStudio WSL alias bash binary conda disk-space docker export-path file-management file-size file-system first-time-setup git global-definitions home-dir homebrew hpc-cluster interface java linux local-machine macOS memory module multi-booting nextflow operating-system ownership package-manager path perl permission-denied permissions processor project-dir prompt python remote-machine root shell-variables singularity softlink source-code storage-quota sudo superuser terminal ubuntu unix windows workdir

• 02: Setting Up Computing Machine
• Operating System (OS) installation
• Getting started with macOS
• Automated batch file operations on Windows
• Windows command-line environments
• Configuring your Linux system
• Various methods of software installation
• Installations on MacBook Pro
• Installations on Windows
• Installations on Linux
• Introduction to UNIX Shell: configuration, variables, home dir
• System info and access permissions
• Superuser command: sudo
• Setting up your home directory for data analysis
• Example .bashrc file configuration

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Filter by tag Filter by tag aria-label="Filter by tag" CLI CLI-navigation CSV JSON PBS SLURM XML aggregate-data algorithm arithmetic array awk bash binary bioawk bioinformatics cmp comm command-piping comparing-files conda count count-words cut cut-characters data-aggregation data-cleaning data-filtering data-formatting data-reshape data-selection data-separator data-splitting dataset dependencies dictionary diff error-handling f-string file-compression file-format file-line-by-line file-operations grep group-by handling-errors hpc-cluster import inputs join-merge library manage-order manual-guide merge-files-by-col module nano numpy object open-close openpyxl outputs package package-manager pandas permissions python raw-data read-write replace-pattern search-pattern sed select-col select-row shell-variables shortcuts sort sort-lines split-data swap-characters syntax-highlighting terminal text-editor text-files tr unix variable vim virtual-env workdir

• Command Line text files editors: nano, vim
• Getting started with UNIX + video + exercises
• Useful text manipulation programs
• GREP – simple search for regular expressions
• SED – replace pattern in stream text
• AWK – advanced text processing
• BIOAWK – biological data manipulation
• DIFF, COMM, CMP – comparing and collating two files with Unix
• UNIX Commands
• Open-Close & Read-Write of data files
• JSON module - encoding & decoding JSON data
• Read, write, split, select data
• Data wrangling: use ready-made apps
• Merge files by common column
• Aggregate data over slicing variations
• Split data or create data chunks

---

Filter by tag Filter by tag aria-label="Filter by tag" Atom BitBucket CLI GUI GitHub IDE Mercurial Midnight Commander OneNote R SVN SciNote Slack VPN VSC artificial-intelligence backup backups bash binary code-archiving code-docs code-editor code-lifecycle code-release code-sharing code-storage code-testing collaboration command comments commit compiler config count-files data-docs data-storage deadline debugger development-environment docs-generator docstring eLabFTW file-list file-manager file-size gcc git goals hosting-platform jupyter knowledge-retention local-repo manage-conflicts markdown note-taking notebook objectives productivity publication pull-updates push-changes python raw-data readme reference-manager remote-repo repository reproducibility source-code standards strategy subversion terminal text-editor timeline workdir

• Basic developer tools
• Integrated & Interactive Development Environment (IDE)
• Visual Studio Code: multi-language integrated DE (VSC)
• PyCharm: IDE for professional Python developers
• Code Development & Management
• Storage & Version Control
• GIT - a distributed version control system
• GIT Commands
• Online hosting platforms for GIT repositories
• Introduction to GitHub
• GitHub - getting started
• GitHub - getting started (class exercise)
• Introduction to BitBucket
• Documentation improvement tools
• A Practical guide to managing research documentation
• Tools for research documentation
• Tools for code documentation
• Monitoring & Evaluation
• Enhancing productivity in research
• Reproducibility in research
• Research reproducibility guideline
• Project Closing
• Research Publication

---

Filter by tag Filter by tag aria-label="Filter by tag" .bashrc .configure .jar .rpm .tar.gz Bioconductor CLI GUI IDE IJulia Makefile OOD PyPI R Vagrant aggregate-data algorithm alias anaconda apptainer chart clustergram-plot cmake code-editor conda container create-container custom-software dendrogram-plot dependencies development-environment docker docker-pull docker-run dplyr file-decompression ggplot github heatmap-plot home-dir hpc-cluster import in-browser inputs interactive-graphing java julia jupyter kernel kubernetes library local-machine macOS markdown math merge-files-by-col modify-container module nextflow notebook numpy openpyxl outputs package package-manager pandas perl permissions pkg plotly project-dir pull-from-docker pull-from-singularity-hub python raw-data remote-machine scatter-plot scipy singularity singularity-build singularity-exec source-code split-data superuser terminal tidyverse venv virtual-env virtual-machine volcano-plot workdir

• Basic developer libraries
• Local Python setup on your computing machine
• Jupyter Lab: create an interactive Python notebook
• Julia setup: installation, environments and Jupyter integration
• Installing custom programs in user space
• Introduction to containers
• Apptainer: the container system for secure HPC
• Singularity
• Creating containers using Singularity
• Modifying existing containers
• Singularity on your Mac via Vagrant
• Docker - accelerated container application development
• Data wrangling: use ready-made apps
• Merge files by common column
• Aggregate data over slicing variations
• Split data or create data chunks
• Plotly graphing - interactive examples in the JupyterLab
• Creating XY scatter plot
• Creating 1D volcano plot
• Creating heatmap
• Creating dendrogram
• Creating clustergram

---

Filter by tag Filter by tag aria-label="Filter by tag" 2D-plot 3D-plot AI ASCII-art Adobe Express Adobe Illustrator Adobe Photoshop Affinity Designer Affinity Photo Apple Numbers BioRender Canva ComplexHeatmap CorelDRAW EPS GIMP GUI Google Charts Google Drawings Google Sheets Heatplus Highcharts IDE Infogram Inkscape JPEG LibreOffice Calc Mind the Graph OOD PDF PNG Piktochart Pixlr R RStudio SSH SVG Sketch SmartDraw TIFF Tableau Public Visme X11-forwarding access-point animation ascii-image-converter ascii-python asciiview audio barplot binary box-plot chart charts clustergram-plot code-editor colab colorscale conda dash data-cleaning data-entry data-exploration data-formatting dataset debugger dendrogram-plot dependencies design development-environment e-signature excel file-format filled-curves ggplot gnuplot graph-layout graphics heatmap heatmap-plot histogram hpc-cluster img2txt import in-browser infographic interactive-graphing jp2a jupyter kernel linux local-machine macOS machine-learning markdown mathplotlib matplotlip mount-folder notebook package-manager pixel plot-data-from-file plot-math-formula plotly python raster raw-data remote-machine scalable scatter-plot scatterplot scientific script-file seaborn spreadsheet sshfs syntax terminal variable vector video virtual-env volcano-plot widgets windows workdir

• Jupyter: interactive web-based multi-kernel DE
• Online Notebook: interactive Python on Try-jupyter and Colab
• Jupyter Lab: create an interactive Python notebook
• RStudio: integrated environment for R programming
• Setting up RStudio
• Viewing graphics in a terminal as the text-based ASCII art
• Mounting remote folder on a local machine
• Manipulating Excel data sheets
• 08: Data Visualization
• Introduction to scientific graphic design
• Raster graphics tools
• Vector graphics tools
• Adobe creative cloud
• Template-based web tools
• Introduction to scientific graphing
• Gnuplot: creating plots in the UNIX Shell
• Gnuplot: variables, loops, conditionals
• Gnuplot: filled curves
• Plotly-Dash: interactive plotting with Python
• Introduction to Plotly
• Introduction to Dash
• Plotly graphing - interactive examples in the JupyterLab
• Creating XY scatter plot
• Creating 1D volcano plot
• Creating heatmap
• Creating dendrogram
• Creating clustergram
• RStudio – data processing & plotting with R
• Creating boxplots in R
• Creating heatmaps in R
• Creating heatmaps in R using ComplexHeatmap