RNA-Seq guide (RNA-seqlopedia)
Gene list analysis
https://gettinggeneticsdone.blogspot.com/2012/03/
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.
ACGT -> Keith Bradnam's blog.
https://twitter.com/JennyBryan (Jenny Bryan)
https://twitter.com/strnr (Stephen Turner)
https://twitter.com/rafalab (Rafa Irizarry)
https://twitter.com/mikelove (Mike Love)
Genome Browser Tutorials
Ensembl Tutorials and Exercises
Command References / Cheatsheets
Bioconductor cheatsheet from HarvardX course
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://it.hms.harvard.edu/our-services/research-computing
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
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