Repositories list

• hci-bio-repository

  Public
  internal scripts for bio-repo management

  Perl

  •

  Artistic License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• OncoTree

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

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• USeq

  Public
  180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capt…

  Java

  •44 forks•1818 stars•11 issue•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• MultiRepMacsChIPSeq

  Public
  Multiple-replica multiple-condition ChIPSeq pipeline

  chip-seqatac-seqchromatin+ 2

  chip-seqatac-seqchromatinmacs2peak-calling

  Perl

  •

  Artistic License 2.0

  •11 fork•66 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• hciR

  Public
  R package for RNA-seq workflows at HCI

  R

  •22 forks•1515 stars•00 issues•00 pull requests•Updated Nov 20, 2025Nov 20, 2025

• hciRdata

  Public
  Datasets for hciR package

  R

  •00 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 7, 2025Nov 7, 2025

• Workflows

  Public
  Snakemake workflows for best practice genomic analysis

  Shell

  •44 forks•77 stars•00 issues•00 pull requests•Updated Oct 28, 2025Oct 28, 2025

• hciR2

  Public
  Extra functions for hciR package

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 3, 2025Oct 3, 2025

• UMIScripts

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

  umibamfastq

  umibamfastq

  Perl

  •

  Artistic License 2.0

  •00 forks•66 stars•00 issues•00 pull requests•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

  •00 forks•11 star•00 issues•11 pull request•Updated Sep 16, 2024Sep 16, 2024

• SubjectMatchMaker

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

  Java

  •00 forks•00 stars•00 issues•00 pull requests•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-analysis+ 3

  restful-apitabixgenomic-data-analysisgquerygenomic-data-scienceregion-search

  C

  •00 forks•22 stars•00 issues•22 pull requests•Updated Apr 14, 2023Apr 14, 2023

• nextflowWorkflow

  Public
  Nextflow

  •11 fork•00 stars•00 issues•00 pull requests•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

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 1, 2022Jul 1, 2022

• hciRscripts

  Public
  R scripts for hciR package

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 26, 2022May 26, 2022

• SBApps

  Public
  Tools for working with the Seven Bridges bioinformatics platform.

  bioinformaticsgenomicscloud-storage+ 2

  bioinformaticsgenomicscloud-storagebioinformatics-dataseven-bridges

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 28, 2021Apr 28, 2021

• RBSSeqTools

  Public
  Java

  •22 forks•11 star•22 issues•00 pull requests•Updated Dec 2, 2020Dec 2, 2020

• Bcode

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 11, 2020Aug 11, 2020

• SB-apps

  Public
  Seven Bridges application tools and workflows

  Common Workflow Language

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 14, 2019Oct 14, 2019

• alademux

  Public
  A la carte demultiplexing with python

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 1, 2019Oct 1, 2019

• atac-counter

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

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 17, 2019Jul 17, 2019

• hci-demux

  Public
  Python

  •00 forks•00 stars•22 issues•00 pull requests•Updated Apr 2, 2019Apr 2, 2019

• scuir

  Public
  Single Cell User Interface with R

  00 forks•11 star•00 issues•00 pull requests•Updated Dec 4, 2017Dec 4, 2017

• MutationScreen

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•66 issues•00 pull requests•Updated Feb 24, 2017Feb 24, 2017

• AutoAligner

  Public
  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2017Jan 4, 2017