25  Bioinformatics and Computational Biology (Part 1)

The Bioinformatics and Computational Biology page offers a curated collection of resources for bioinformatics and computational biology. The page includes personal and lab websites, tutorials, courses, books, and projects.

25.1 Personal Blogs and Lab Websites

25.1.1 Blogs

  1. JT Leek
  2. Karolis Koncevičius
  3. Eytan Ruppin
  4. Lior Pachter
  5. Jean Fan
  6. Philip Compeau
  7. Karl Broman
  8. Ming Tang
  9. James Zou
  10. Tyler Burns
  11. Jeffrey Grover
  12. Sung Rye Park

25.1.2 Lab Websites

  1. Krishnaswamy Lab
  2. Liu Lab
  3. Costa Lab
  4. ZHOU LAB
  5. Childhood Cancer Data Lab
  6. Ma’ayan Lab
  7. Ty Miller Lab
  8. Griffith Lab Teaching

25.1.3 Bioinformatics Consulting Companies

  1. Independent Data Lab

25.2 Curated list of resources and Datasets

  1. Glittr: curated list of bioinformatics training material
  2. Collection of bioinformatics training materials
  3. Genomics and Bioinformatics Resources
  4. Cell and Gene Datasets
  5. Recommended Awesome Lists for Bioconductor Community
  6. Biostars
  7. SEQanswers

25.3 Bioinformatics News Stories

  1. GENOMES ARISING
  2. The next chapter for African genomics

25.4 Bioinformatics Basics

25.4.1 Background Notes

  1. Fundamentals of Bioinformatics
  2. RNA-Seq: The Cells Librarian
  3. Single cell sequencing: what it is and why researchers in industry and academia want it
  4. What is Bioinformatics?
  5. Bioinformatics Tutorials by Digital World Biology
  6. Bioinformatics Education and Tutorials
  7. []

25.4.2 Courses and Lectures

  1. Introduction to Genomics for Engineers
  2. Introduction to Computational Biology
  3. SDS 348, Computational Biology and Bioinformatics 2019
  4. SDS 348, Computational Biology and Bioinformatics 2020
  5. BMI 702: Biomedical Artificial Intelligence
  6. DIY Transcriptomics
  7. BIG Bioinformatics
  8. Intro to Biomedical Data Science
  9. Introduction to Unix, Orchestra and RNA-Seq
  10. Linux command line exercises for NGS data processing
  11. Introduction to Unix
  12. Engineering Biology Research Consortium
  13. Genomic Data Science Community Network
  14. Learn about Bioinformatics and Computational Tools for Biology
  15. Introduction to R for Biologists
  16. Graphs and Networks for Biology using R
  17. HBC Training Program Basic Data Skills
  18. Caltech BI/BE/CSS 183: Introduction to Computational Biology and Bioinformatics
  19. Genomic Data Visualization
  20. BILD62 (Intro to Python for Biologists)
  21. RaukR 2022: Advanced R for Bioinformatics
  22. RaukR 2023: Advanced R for Bioinformatics
  23. HTS2018 resources
  24. GSEAtraining
  25. Bioinformatics for Beginners: RNA-Seq
  26. LINCS Workflow
  27. The RNA-seqlopedia
  28. Great Ideas in Computational Biology
  29. RNA-seq Bioinformatics Course
  30. Genomic Data Visualization and Interpretation
  31. Precision Medicine Biology
  32. RNA-seq Bioinformatics Course: All Lectures
  33. Infectious Disease Genomic Epidemiology 2024

25.4.3 Books and Resources

  1. Welcome to a Little Book of R for Bioinformatics

  2. Modern Statistics for Modern Biology

  3. Learning Bioinformatics At Home

  4. Important numbers in Cell Biology

  5. The Biologist’s Guide to Computing

  6. Bioinformatics Starter Pack

  7. Orchestrating Single-Cell Analysis with Bioconductor

  8. Single-cell best practices

  9. Biodatascience101

  10. Introduction to biological circuit design

  11. Biological Architecture Reading Roadmap

  12. RNA-Seq Blog

  13. 7 Books for you to learn bioinformatics

  14. Biomedical Data Science Book

  15. Best Practices for Spatial Transcriptomics Analysis with Bioconductor

  16. Data Science for the Biomedical Sciences

  17. What is genomics?

  18. COLAUTTI LAB Books and Resources

  19. 20 YouTube Channels Every Bioinformatician Should Follow

  20. Data Analysis for the Life Sciences (Free E-book)

  21. Practical Computing for Biologists

  22. Bioinformatics Data Skills (2015)

  23. The Supplementary Material Repository for Bioinformatics Data Skills

  24. From cell line to command line

  25. A Primer for Computational Biology

  26. Computational Genomics with R

  27. The Biostar Handbook. A bioinformatics e-book for beginners

  28. Cleva Lab Biology

  29. Folding@Home

  30. Python for biologists

  31. Modeling Life

  32. Fundamentals of computational biology

  33. Learn Bioinformatics in 100 hours

  34. Bioinformatics Training & Education Program

  35. Bioinformatics Workbook

  36. My opinionated selection of books/urls for bioinformatics/data science curriculum

  37. Statistical Modeling of High Dimensional Counts

  38. Genomics Boot Camp

  39. Deep learning on computational biology and bioinformatics tutorial

  40. ILRI Bioinformatics Resources

  41. NIH Data Science Resources

  42. Resources to become a computational biologist outside of academia

  43. Pandora Bioinformatics Resources

  44. CRISPRpedia

  45. QUBES: Network for Integrating Bioinformatics into Life Sciences Education

  46. Next-Generation Sequencing Analysis Resources

  47. Biomedical Knowledge Mining using GOSemSim and clusterProfiler

  48. Biological Modeling

  49. Bioconductor Books

25.4.4 Tools and Pipelines

  1. R2 Genomics Analysis and Visualization Platform
  2. BeGenomics Tutorials
  3. BD2K-LINCS DATA COORDINATION AND INTEGRATION CENTER
  4. The Top 15 Machine Learning Data Science Bioinformatics Open Source Projects
  5. Biopython
  6. gget
  7. ROSALIND
  8. Free and Open Source Tools for Bioinformatics and Molecular Biology
  9. PiGx: Pipelines in Genomics
  10. USC Libraries Bioinformatics
  11. NCI Bioinformatics Training and Education Program
  12. Harvard Chan Bioinformatics Core
  13. Genomic Data Processing
  14. Machine Learning in Genomics Workshop
  15. Bioconductor
  16. UConn File Formats Tutorial
  17. The Molecular Map of Exercise
  18. ShinyGO
  19. Scimap: scalable toolkit for analyzing spatial molecular data
  20. Docker Image of DIYTranscriptomics (password-protected)
  21. Enrichr
  22. Bedtools
  23. Salmon
  24. kallisto
  25. Getting Started with Seurat

25.5 Bioinformatics Tutorials and Projects

25.5.1 Tutorials

  1. Oncology Bioinformatics project tutorial

  2. Centre of Bioinformatics Research and Technology (CBIRT)

  3. Crash Courses in Bioinformatics

  4. Data Carpentry for Biologists

  5. Illustrating Python via Examples from Bioinformatics

  6. Illustrating Python via Bioinformatics Examples

  7. EVOLUTION AND GENOMICS

  8. Bioinformatics Introduction

  9. Griffith Lab Tutorials and Courses

  10. PCA in action

  11. A Primer on Deep Learning in Genomics

  12. Bioinformatics Tutorials

  13. Free online training in bioinformatics and biostatistics

  14. Bioinformatics Midterm Project

  15. Introduction to bioinformatics

  16. Explore the world of Bioinformatics with Machine Learning

  17. Bioinformatics for Dummies: A Beginner’s Quick Guide

  18. Interactive Bioinformatics Tutorials

  19. Ming Tang Comp Bio Tutorials

  20. Bioinformatics Documentation from Melbourne

  21. Bioinformatics Introduction

  22. Data Carpentry - Genomics Workshop

  23. Open source bioinformatics tutorials

  24. Introduction to Network Analysis in Systems Biology

25.5.2 Tips and Troubleshooting

  1. How I transitioned from biologist to biology-leveraged bioinformatician
  2. fastq-dump command not found

25.5.3 Program-specific tutorials

25.5.3.1 Tidyverse and R in Bioinformatics

  1. Bioinformatics in the Tidyverse
  2. An Introduction to R through the tidyverse + Bioinformatics
  3. R for Biology Data Science
  4. Intro to R and RStudio for Genomics
  5. The Bioconductor 2018 Workshop Compilation
  6. Bioconductor Workshop 1 Jupyter Notebooks
  7. MicroArray Project
  8. An Introduction to R through the tidyverse

25.5.3.2 Python

  1. First Steps in Biopython
  2. What is BioPython
  3. Getting Started with Biopython
  4. Biopython Tutorial
  5. Practical Computing for Biologists
  6. Biopython Tutorial and Cookbook
  7. Single Cell Transcriptomics with Python
  8. Stellenbosch: Introduction to Python for Bioinformatics

25.5.3.3 Linux, Command Line, and Git

  1. Introduction to Linux for bioinformatics
  2. Bioinformatics one-liners
  3. Unix & Perl Primer for Biologists
  4. Happy Belly Bioinformatics - Unix home
  5. Bioinformatics Tutorials: The command-line
  6. Bash basics
  7. Git basics
  8. Introduction to the Unix Shell for Bioinformatics
  9. Introduction to Unix
  10. Entrez Direct: E-utilities on the Unix Command Line

25.5.3.4 Galaxy

  1. Galaxy
  2. Galaxy Machine Learning Community
  3. Reference-based RNA-Seq data analysis
  4. Galaxy Training

25.5.3.5 Workflows

  1. Seqera
  2. NextFlow
  3. Script of Scripts (SoS)
  4. An Introduction to Snakemake for Bioinformatics
  5. bioBakery Workflows
  6. The Snakemake Tutorial I Wish I Had
  7. On Bioinformatics Workflow Design
  8. Conda Setup

25.5.4 Cancer Genomics

  1. Open Pediatric Brain Tumor Atlas
  2. OpenPBTA Paper
  3. Big Data Training for Cancer Research
  4. Genomic Data Commons
  5. Childhood Cancer Data Lab Workshop Materials
  6. Childhood Cancer Data Lab Research Resources
  7. Introduction to R for Cancer Scientists
  8. St. Jude Cloud Genomics Platform
  9. Cancer Research Resources
  10. cBioPortal Google Summer of Code (GSoC)
  11. A deep profile of gene expression across 18 human cancers
  12. Tumor Classification PCA
  13. Gene Expression Analysis in R workshop 2022

25.5.5 Bulk Omics

  1. conquer (consistent quantification of external RNA-seq data sets)
  2. RNA-seq Bioinformatics Resources
  3. RNA Seq analysis tutorial
  4. Thinking about Designing RNA Seq Experiments to Measure Differential Gene Expression: The Basics
  5. RNA-Seq Blog
  6. Importing transcript abundance with tximport
  7. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
  8. RNA-seq workflow: gene-level exploratory analysis and differential expression

25.5.6 Single Cell Omics

  1. scRNA seq pipeline with one file
  2. Single-cell sequencing analysis: the importance of data integration
  3. Run CyTOF analysis with Seurat
  4. Mapping and annotating query datasets
  5. How Difficult Is It To Start Your Single-cell Analysis As A Beginner
  6. Seurat - Guided Clustering Tutorial
  7. Scanpy tutorials
  8. Single cell studies database
  9. Using SingleR to annotate single-cell RNA-seq data
  10. Seurat Command List

25.5.7 Spatial Omics

  1. An open and universal framework for processing spatial omics data
  2. Exploring Spatial Omics
  3. Analysis and visualization of spatial transcriptomics data
  4. Analysis, visualization, and integration of spatial datasets with Seurat
  5. Spatial omics takes off
  6. Two platforms, one powerful spatial biology toolkit

25.5.8 Projects

  1. Analysing the HIV pandemic, Part 1: HIV in sub-Sahara Africa
  2. Analysing the HIV pandemic, Part 2: Drug resistance testing
  3. Analysing the HIV pandemic, Part 3: Genetic diversity
  4. Analysing the HIV pandemic, Part 4: Classification of lab samples
  5. Machine learning for biology part one
  6. Machine learning for biology part two
  7. Machine learning for biology part three
  8. Machine learning for biology part four

25.5.9 Crowdsourcing Bioinformatics

  1. Bioinformatics Research Network
  2. Bioinformatics Research Network Skill Assessments
  3. Huang Lab: Precision Omics
  4. Stimulating Innovation in Breast Cancer Genetic Epidemiology
  5. BD2K-LINCS Data Coordination and Integration Center: Crowdsourcing Portal
  6. DREAM Challenges
  7. Figure One Lab
  8. Coding Exercise: TCGA