Software and Data

Benayoun Laboratory Github repository

Functional enrichment analysis portals:

• DAVID
• Enrichr
• GREAT
• GOrilla (mHG statistics use)
• GSEA/MSigDB
• ProfileChaser (Profile Comparison to GEO)
• GeneChaser

Other useful online bioinformatics tools:

• NCBI BLAST
• Expasy Proteomics Tools
• BioMart (gene annotation information export)
• ClustalOmega (Multiple sequence alignment)

Free standalone bioinformatics software:

• NML library at USC
• HOMER (NGS analysis software suite)
• RStudio (Free IDE for R)
• NGSplot
• piPIPES (transposon and piRNA analysis pipelines)
• MACS2 (ChIP-seq peak caller)
• CEAS (Genomic region annotations)

R programming tips:

• R statistical software
• Bioconductor (Repository for biology R packages )
• R Graph Gallery (plotting recipes)