Links

Publicly available genomics datasets

• NCBI Gene Expression Omnibus
• ENCODE @ UCSC
• Roadmap Epigenomics
• modMINE

Genome browsers

• USCC Genome Browser
• WashU Epigenome Browser
• IGV

Analysis pipelines/suites

• Galaxy
• The MEME Suite

Motif finders

• AlignACE
• MEME
• HOMER
• Weeder
• MotifSpec

ChIP-seq peak callers

• MACS
• PeakSeq

Functional annotation

• GREAT
• DAVID
• GoStat