Books

1. Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools
2. Bioinformatics and Functional Genomics
3. Practical Computing for Biologists
4. The Biostar Handbook
5. Computational Biology A Practical Introduction to BioData Processing and Analysis with Linux, MySQL, and R

R

1. R for Data Science: Import, Tidy, Transform, Visualize, and Model Data
2. ggplot2: Elegant Graphics for Data Analysis (Use R!)

Python

1. Learning Python

Bash

1. iterm2
2. awk
3. sed
4. bio Syntax

Blogs

1. (https://rna-seqblog.com)
2. (http://www.longwoodgenomics.org/)
3. (https://liorpachter.wordpress.com/)
4. (https://davetang.org/)
5. (http://onetipperday.sterding.com/)

bioconductor

1. biocworkshop
2. Data Analysis in Genome Biology
3. Biomedical Data Science
4. Introduction to Computational Biology
5. Gviz

Tools

1. bwt
2. bedtools, Applied Computational Genomics Course
3. bedtools, cheatsheet
4. Snakemake

papers

• RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
• Modeling and analysis of RNA-seq data: a review from a statistical perspective
• A survey of best practices for RNA-seq data analysis
• RNA sequencing: the teenage years

Course

• applied-computational-genomics

Collections

• sib-swiss
• Ming Tang