Online computing and analysis resources I've found useful for my research at at some point.
- Current Topics in Genomics 2014 lectures from the NIH
- Statistics visualizations by Emil Kirkegaard
- Plotting in R: by Claus Wilke and Hadley Wickham
- R Reference Card by Tom Short
- R for beginners by Emmanuel Paradis
- Statistics for Biologists collection at Nature
- Homebrew - For downloading/installing on Mac. Original code by Max Howell, Website by Remi Prevost.
- Perl 5 By Example - Intro to programming in perl. By David Medinets.
- vi cheat sheet by Lagmonster.
Parsing and Analysis
- Bedtools: Dealing with Bed files, by Aaron Quinlan
- PGDSpider: Conversion tool for population genomics data types.
- Galaxy: Open source, web-based platform for data intensive biological research.
- DAVID: Database for Annotation, Visualization and Integrated Discovery
- GORILLA: Gene Ontology enRIchment anaLysis and visuaLizAtion tool
- Databases for teaching: Ernest, Morgan; Brown, James; Valone, Thomas; White, Ethan P. (2015): Portal Project Teaching Database
Viewing phylogenetic trees
- FigTree by Andrew Rambaut (cite website).
- ITOL: Interactive Tree of Life by Letunic and Bork (2007).
- Dendroscopeby Daniel H. Hudson (paper here).
For browsing: more comprehensive collections of bioinformatics resources
- ExPASy Bioinformatics Resource Portal
- Bioinformatics Resources collected by Anil Jegga
- Online Bioinformatics Resources Collection (OBRC) by the Health Sciences Library System at the University of Pittsburgh
Writing and Publishing