Biostar Tutorial: Cheat sheet for one-based vs zero-based coordinate systems
Biostar Tutorial: Cheat sheet for one-based vs zero-based coordinate systems Obi Griffith over at Biostar put together this excellent cheat sheet for dealing with one-based and zero-based genomic coordinate systems. The cheat sheet visually explains the difference between zero and one-based coordinate systems, as well as how to indicate a position, SNP, range, or indel using both coordinate system
Sync Your Rprofile Across Multiple R Installations
Your Rprofile is a script that R executes every time you launch an R session. You can use it to automatically load packages, set your working directory, set options, define useful functions, and set up database connections, and run any other code you want every time you start R. If you're using R in Linux, it's a hidden file in your home directory called ~/.Rprofile, and if you're on Windows, it's
Resources for Pathway Analysis, Functional Annotation, and Interactome Reconstruction with Omics Data
Resources for Pathway Analysis, Functional Annotation, and Interactome Reconstruction with Omics Data I just read a helpful paper on pathway analysis and interactome reconstruction: Tieri, P., Fuente, A. D., Termanini, A., & Franceschi, C. (2011). Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis. In Bioinformatics for Omics Data, Methods in Molecul
GWAS Manhattan plots and QQ plots using ggplot2 in R
**** UPDATE, May 15 2014 ***** The functions described here have now been wrapped into an R package. View the updated blog post or see the online package vignette for how to install and use. If you'd still like to use the old code described here, you can access this at version 0.0.0 on GitHub. The code below likely won't work. ***************************** Will posted earlier this week about how t
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Real-time streaming differential RNA-seq analysis with eXpress
Annotated Manhattan plots and QQ plots for GWAS using R, Revisited
PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data
Download 69 Complete Human Genomes
Video and slides from ASHG 1000 Genomes tutorials
Using Expression Data to Mine the "Gray Zone" of GWAS