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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 filesGQuery
GQuery is a software tool for rapidly querying large numbers of bgzip compressed, tabix indexed genomic data files e.g. vcf, maf, bed, bedGraph, etc. from multiple species with different genome builds without the need to develop, debug, and maintain custom file parsers. Search for particular germline or somatic mutations, copy number changes, differentially expressed genes, epigenetic marks, anything that can be associated with genomic coordinates. Just point the GQuery indexer at a collection of tabix indexed files and then run either the GQuery command line app or the web API to search them. GQuery is built using a fast, multi-threaded, genomic range search engine with extensive junit testing.scuir
Single Cell User Interface with Ratac-counter
Alternative counting for 10x Genomics single cell ATAC-seq dataLove Open Source and this site? Check out how you can help us