Software

COHCAP - City of Hope CpG Island Analysis Pipeline

• Ideal for Illumina 450k Methylation Array Data (but can use custom annotations for EPIC Array, BS-Seq, etc.)
• Also available as a Bioconductor package (which is what I strongly recommend using)

BD-Func - Bidirectional Functional Enrichment

• Pre-defined gene lists for analysis of human and mouse gene expression data

sRAP - Simplified RNA-Seq Analysis Pipeline

• NOTE: I have switched to using templates for most analysis, where some (slightly outdated) examples are on GitHub (including the RNA-Seq templates, with the warning that I think the "templates" are really an intermediate step towards the most appropriate long-term solution). These templates require a little greater familiarity with coding than sRAP (and, in terms of the general strategy - it is usually easier to edit your own code than other's code; so, I can't provide support for other people to use these scripts), but I typically find the flexibility to edit the templates better for specific projects. So, I would typically not recommend use of sRAP.