Pinned Repositories
atac-counter
Alternative counting for 10x Genomics single cell ATAC-seq data
AwsApps
Genomic data focused toolkit for working with Amazon AWS S3 and EC2
GQuery
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.
hciR
R package for RNA-seq workflows at HCI
MultiRepMacsChIPSeq
Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
RBSSeqTools
scuir
Single Cell User Interface with R
UMIScripts
Simple scripts for handling Unique Molecular Indexes in Fastq and Bam files
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.
Workflows
Snakemake workflows for best practice genomic analysis
Huntsman Cancer Institute's Repositories
HuntsmanCancerInstitute/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.
HuntsmanCancerInstitute/hciR
R package for RNA-seq workflows at HCI
HuntsmanCancerInstitute/MultiRepMacsChIPSeq
Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
HuntsmanCancerInstitute/Workflows
Snakemake workflows for best practice genomic analysis
HuntsmanCancerInstitute/UMIScripts
Simple scripts for handling Unique Molecular Indexes in Fastq and Bam files
HuntsmanCancerInstitute/GQuery
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.
HuntsmanCancerInstitute/atac-counter
Alternative counting for 10x Genomics single cell ATAC-seq data
HuntsmanCancerInstitute/AwsApps
Genomic data focused toolkit for working with Amazon AWS S3 and EC2
HuntsmanCancerInstitute/RBSSeqTools
HuntsmanCancerInstitute/scuir
Single Cell User Interface with R
HuntsmanCancerInstitute/AutoAnalysis
AutoAnalysis orchestrates auto analysis of sequencing files in GNomEx Experiment using two different daemons running on HCI and CHPC servers. This is a custom toolkit for internal use at the University of Utah.
HuntsmanCancerInstitute/SBApps
Tools for working with the Seven Bridges bioinformatics platform.
HuntsmanCancerInstitute/SubjectMatchMaker
Master human subject ID generator and matcher based on PHI keys - name, dob, gender, mrn
HuntsmanCancerInstitute/10xranger-nf
A Nextflow wrapper for 10X Cellranger and spaceranger to wrangle the 10,000+ output files per sample
HuntsmanCancerInstitute/alademux
A la carte demultiplexing with python
HuntsmanCancerInstitute/AutoAligner
HuntsmanCancerInstitute/Bcode
HuntsmanCancerInstitute/BioMinerQT
The BioMiner Query Tool is a multi-omic, cross species, web-app that ingests ChIP/RNA/Bisulfite/Variant-Seq analysis and enables users to perform iterative searches to identify records based on region or gene name.
HuntsmanCancerInstitute/hci-bio-repository
internal scripts for bio-repo management
HuntsmanCancerInstitute/hci-demux
HuntsmanCancerInstitute/hciR2
Extra functions for hciR package
HuntsmanCancerInstitute/hciRdata
Datasets for hciR package
HuntsmanCancerInstitute/hciRscripts
R scripts for hciR package
HuntsmanCancerInstitute/MutationScreen
HuntsmanCancerInstitute/nextflowWorkflow
HuntsmanCancerInstitute/SB-apps
Seven Bridges application tools and workflows