Resources

Blog posts

RNA-Seq guide (RNA-seqlopedia)

http://rnaseq.uoregon.edu/

Gene list analysis:

http://www.gettinggeneticsdone.com/2012/03/pathway-analysis-for-high-throughput.html

Creating a reproducible workflow:

http://kbroman.org/steps2rr/

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.

https://twitter.com/JennyBryan (Jenny Bryan)

https://twitter.com/genetics_blog (Stephen Turner)

https://twitter.com/rafalab (Rafa Irizarry)

https://twitter.com/mikelove (Mike Love)

Genome Browser Tutorials

Ensembl Tutorials and Exercises

IGV Tutorials

UCSC Tutorials at OpenHelix

UCSC Guide: eBook in Nature

Unix shell command reference

The art of the command line

VI / VIM command reference

R cheatsheets

Bioconductor cheatsheet from HarvardX course

Basic Git cheatsheet

Templates

Template to keep track of RNA-Seq reads

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

HMS Research Computing: https://wiki.med.harvard.edu/Orchestra/UserTraining

FAS Research Computing: https://rc.fas.harvard.edu/training/ (special interest might include the "Tips at 12")

Countway Library: https://www.countway.harvard.edu/classes-events

Institute for Quantitative Social Sciences: http://projects.iq.harvard.edu/rtc/calendar/upcoming

HarvardX course "Statistics and R for the Life Sciences": https://courses.edx.org/courses/HarvardX/PH525.1x/1T2015/info

• More materials from this class: http://genomicsclass.github.io/book/

Broad Institute: http://www.broadinstitute.org/partnerships/education/broade/broad-workshops

Online Bioinformatics Training Resources

DataCamp Intermediate R course: https://www.datacamp.com/courses/intermediate-r

DataCamp Data Visualization with ggplot2: https://www.datacamp.com/courses/data-visualization-with-ggplot2-1

Bioconductor for Genomic Data Science (Kasper Hansen)

scRNA-Seq Heterogeneity analysis (Jean Fan)

Guide to kits for library preparation

From genohub: https://genohub.com/ngs-library-preparation-kit-guide/

Literature

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