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    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 t…
      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, capt…
      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•6•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 multi…
      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 sear…
      Java
      •0•0•6•0•Updated Feb 24, 2017Feb 24, 2017

    • AutoAligner

      Public
      Java
      •0•0•0•0•Updated Jan 4, 2017Jan 4, 2017