Repositories list

• USeq

  Public
  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.

  Java

  •4•17•1•0•Updated Dec 30, 2024Dec 30, 2024

• AutoAnalysis

  Public
  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.

  Java

  •1•0•0•0•Updated Dec 30, 2024Dec 30, 2024

• hciR

  Public
  R package for RNA-seq workflows at HCI

  R

  •1•13•0•0•Updated Dec 9, 2024Dec 9, 2024

• Workflows

  Public
  Snakemake workflows for best practice genomic analysis

  Shell

  •4•7•0•0•Updated Dec 2, 2024Dec 2, 2024

• hci-bio-repository

  Public
  internal scripts for bio-repo management

  Perl

  •

  Artistic License 2.0

  •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

• MultiRepMacsChIPSeq

  Public
  Multiple-replica multiple-condition Macs2 ChIPSeq wrapper

  chip-seqatac-seqchromatin+ 2macs2peak-calling

  Perl

  •

  Artistic License 2.0

  •1•7•0•0•Updated Nov 1, 2024Nov 1, 2024

• UMIScripts

  Public
  Simple scripts for handling Unique Molecular Indexes in Fastq and Bam files

  umibamfastq

  Perl

  •

  Artistic License 2.0

  •0•6•0•0•Updated Oct 28, 2024Oct 28, 2024

• AwsApps

  Public
  Genomic data focused toolkit for working with Amazon AWS S3 and EC2

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•1•Updated Sep 16, 2024Sep 16, 2024

• hciRdata

  Public
  Datasets for hciR package

  R

  •0•0•0•0•Updated Jun 20, 2024Jun 20, 2024

• SubjectMatchMaker

  Public
  Master human subject ID generator and matcher based on PHI keys - name, dob, gender, mrn

  Java

  •0•0•0•0•Updated May 3, 2024May 3, 2024

• hciR2

  Public
  Extra functions for hciR package

  R

  •0•0•0•0•Updated Dec 20, 2023Dec 20, 2023

• GQuery

  Public
  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, di…

  restful-apigenomic-data-analysisgquery+ 3genomic-data-scienceregion-searchtabix

  C

  •0•2•0•2•Updated Apr 14, 2023Apr 14, 2023

• nextflowWorkflow

  Public
  Nextflow

  •1•0•0•0•Updated Aug 18, 2022Aug 18, 2022

• 10xranger-nf

  Public
  A Nextflow wrapper for 10X Cellranger and spaceranger to wrangle the 10,000+ output files per sample

  Nextflow

  •

  MIT License

  •2•0•0•0•Updated Jul 1, 2022Jul 1, 2022

• hciRscripts

  Public
  R scripts for hciR package

  R

  •0•0•0•0•Updated May 26, 2022May 26, 2022

• SBApps

  Public
  Tools for working with the Seven Bridges bioinformatics platform.

  bioinformaticsgenomicscloud-storage+ 2bioinformatics-dataseven-bridges

  Java

  •0•0•0•0•Updated Apr 28, 2021Apr 28, 2021

• RBSSeqTools

  Public
  Java

  •2•1•2•0•Updated Dec 2, 2020Dec 2, 2020

• Bcode

  Public
  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 11, 2020Aug 11, 2020

• SB-apps

  Public
  Seven Bridges application tools and workflows

  Common Workflow Language

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 14, 2019Oct 14, 2019

• alademux

  Public
  A la carte demultiplexing with python

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 1, 2019Oct 1, 2019

• atac-counter

  Public
  Alternative counting for 10x Genomics single cell ATAC-seq data

  Python

  •

  MIT License

  •0•1•0•0•Updated Jul 17, 2019Jul 17, 2019

• hci-demux

  Public
  Python

  •0•0•2•0•Updated Apr 2, 2019Apr 2, 2019

• scuir

  Public
  Single Cell User Interface with R

  0•1•0•0•Updated Dec 4, 2017Dec 4, 2017

• MutationScreen

  Public
  Python

  •0•0•0•0•Updated Aug 11, 2017Aug 11, 2017

• BioMinerQT

  Public
  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.

  Java

  •0•0•6•0•Updated Feb 24, 2017Feb 24, 2017

• AutoAligner

  Public
  Java

  •0•0•0•0•Updated Jan 4, 2017Jan 4, 2017