Skip to content

@HuntsmanCancerInstitute Huntsman Cancer Institute - Cancer Bioinformatics Shared Resource

Change the repository type filter

All

    Repositories list

    27 repositories

    • hci-bio-repository

      Public
      internal scripts for bio-repo management
      Perl
      •
      Artistic License 2.0
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • Playdon-Hardikar-Lab

      Public
      Code and file repo for projects in Dr. Mary Playdon's and Dr. Sheetal Hardikar's laboratories
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • hciR

      Public
      R package for RNA-seq workflows at HCI
      R
      •1•14•0•0•Updated Nov 20, 2025Nov 20, 2025

    • hciRdata

      Public
      Datasets for hciR package
      R
      •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • 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 Nov 7, 2025Nov 7, 2025

    • 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•18•1•0•Updated Nov 6, 2025Nov 6, 2025

    • Workflows

      Public
      Snakemake workflows for best practice genomic analysis
      Shell
      •4•7•0•0•Updated Oct 28, 2025Oct 28, 2025

    • hciR2

      Public
      Extra functions for hciR package
      R
      •0•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • MultiRepMacsChIPSeq

      Public
      Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
      chip-seqatac-seqchromatinmacs2peak-calling
      Perl
      •
      Artistic License 2.0
      •1•7•0•0•Updated Aug 5, 2025Aug 5, 2025

    • 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

    • 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

    • 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-apitabixgenomic-data-analysisgquerygenomic-data-scienceregion-search
      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-storagebioinformatics-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