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@HuntsmanCancerInstitute

Huntsman Cancer Institute - Cancer Bioinformatics Shared Resource

The Cancer Bioinformatics Shared Resource (CBI) supports both research and translational bioinformatics at HCI.

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  1. USeq 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 …

    Java 19 4

  2. hciR hciR Public

    R package for RNA-seq workflows at HCI

    R 15 2

  3. Workflows Workflows Public

    Snakemake workflows for best practice genomic analysis

    Shell 7 4

  4. MultiRepMacsChIPSeq MultiRepMacsChIPSeq Public

    Multiple-replica multiple-condition ChIPSeq pipeline

    Perl 6 1

  5. GQuery 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 bui…

    C 2

  6. AwsApps AwsApps Public

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

    Java 1

Repositories

Showing 10 of 28 repositories
  • hci-bio-repository Public

    internal scripts for bio-repo management

    HuntsmanCancerInstitute/hci-bio-repository's past year of commit activity
    Perl 0 Artistic-2.0 0 0 0 Updated Oct 8, 2026
  • 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.

    HuntsmanCancerInstitute/AutoAnalysis's past year of commit activity
    Java 0 1 0 0 Updated Oct 2, 2026
  • 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.

    HuntsmanCancerInstitute/USeq's past year of commit activity
    Java 19 4 1 0 Updated Sep 30, 2026
  • OncoTree Public

    Apps for working with and classifying tumors according to MSK's OncoTree platform

    HuntsmanCancerInstitute/OncoTree's past year of commit activity
    Java 0 MIT 0 0 0 Updated Sep 30, 2026
  • UMIScripts Public

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

    HuntsmanCancerInstitute/UMIScripts's past year of commit activity
    Perl 6 Artistic-2.0 0 0 0 Updated Jul 23, 2026
  • Workflows Public

    Snakemake workflows for best practice genomic analysis

    HuntsmanCancerInstitute/Workflows's past year of commit activity
    Shell 7 4 0 0 Updated May 13, 2026
  • MultiRepMacsChIPSeq Public

    Multiple-replica multiple-condition ChIPSeq pipeline

    HuntsmanCancerInstitute/MultiRepMacsChIPSeq's past year of commit activity
    Perl 6 Artistic-2.0 1 0 0 Updated May 12, 2026
  • Playdon-Hardikar-Lab Public

    Code and file repo for projects in Dr. Mary Playdon's and Dr. Sheetal Hardikar's laboratories

    HuntsmanCancerInstitute/Playdon-Hardikar-Lab's past year of commit activity
    Jupyter Notebook 0 BSD-2-Clause 0 0 0 Updated Dec 12, 2025
  • hciR Public

    R package for RNA-seq workflows at HCI

    HuntsmanCancerInstitute/hciR's past year of commit activity
    R 15 2 0 0 Updated Nov 20, 2025
  • hciRdata Public

    Datasets for hciR package

    HuntsmanCancerInstitute/hciRdata's past year of commit activity
    R 0 0 0 0 Updated Nov 20, 2025
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