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USeq
180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.hciR
R package for RNA-seq workflows at HCIMultiRepMacsChIPSeq
Multiple-replica multiple-condition Macs2 ChIPSeq wrapperWorkflows
Snakemake workflows for best practice genomic analysisUMIScripts
Simple scripts for handling Unique Molecular Indexes in Fastq and Bam filesscuir
Single Cell User Interface with RRBSSeqTools
atac-counter
Alternative counting for 10x Genomics single cell ATAC-seq dataLove Open Source and this site? Check out how you can help us