Bioinformatic Training Resources

RNA-Seq guide (RNA-seqlopedia)

Gene list analysis

Creating a reproducible workflow

General Bioinformatics, Benchmarking and Personal opinions

Blue Collar Bioinformatics -> bcbio group's blog.

Bits of DNA -> Lior Pachter's blog.

Living in an Ivory Basement -> C. Titus Brown's blog.

The Tree of Life -> Jonathan Eisen's blog. 

Getting Genetics Done -> Stephen Turner's blog.

ACGT -> Keith Bradnam's blog. (Jenny Bryan) (Stephen Turner) (Rafa Irizarry) (Mike Love)

Genome Browser Tutorials

Ensembl Tutorials and Exercises

IGV Tutorials

UCSC Tutorials at OpenHelix

UCSC Guide: eBook in Nature

Command References / Cheatsheets

Unix shell command reference

The art of the command line

VI / VIM command reference

R cheatsheets

Bioconductor cheatsheet from HarvardX course

Basic Git cheatsheet


Template to keep track of RNA-Seq reads

Harvard Bioinformatics Training Resources (including Python, R, Perl, Genome Database, Genome Browser workshops)

HMS Research Computing:

FAS Research Computing: (special interest might include the "Tips at 12")

Countway Library:

Institute for Quantitative Social Sciences:

HarvardX course "Statistics and R for the Life Sciences":

Broad Institute:

Online Bioinformatics Training Resources

DataCamp Intermediate R course:

DataCamp Data Visualization with ggplot2:

Bioconductor for Genomic Data Science (Kasper Hansen)

scRNA-Seq Heterogeneity analysis (Jean Fan)

Guide to kits for library preparation

From genohub:


"A survey of best practices for RNA-seq data analysis" Conesa et al., Genome Biology 2016 17:13