Repositories list

• pan_cancer_paper

  Public
  Pan-cancer CNA paper

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• tnbc-chemo

  Public
  Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy

  chemotherapybreast-cancerscrna+ 4

  chemotherapybreast-cancerscrnavisiumtnbcxeniumvisium-hd

  R

  •00 forks•33 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• Copykit_manuscript_code

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• CopyKit_paper

  Public
  Scripts to reproduce the figures from the CopyKit manuscript

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 9, 2026Jan 9, 2026

• wellDA-seq

  Public
  Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer

  R

  •00 forks•11 star•11 issue•00 pull requests•Updated Dec 30, 2025Dec 30, 2025

• copykit

  Public
  Toolkit for single-cell copy number analysis

  R

  •

  Other

  •55 forks•3333 stars•33 issues•00 pull requests•Updated Dec 15, 2025Dec 15, 2025

• copykat

  Public
  R

  •

  Other

  •6464 forks•277277 stars•6969 issues•22 pull requests•Updated Oct 13, 2025Oct 13, 2025

• DCIS_TME

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 18, 2025Sep 18, 2025

• wellDR-seq

  Public
  Code deposit for wellDR-seq paper

  R

  •22 forks•55 stars•11 issue•00 pull requests•Updated Sep 14, 2025Sep 14, 2025

• B7-H3

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 9, 2025Sep 9, 2025

• CSHL_workshops

  Public
  33 forks•66 stars•00 issues•00 pull requests•Updated May 1, 2025May 1, 2025

• intro_bioinfo_course

  Public
  introduction to bioinformatics workshop

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2025Apr 14, 2025

• PRECISE_paper

  Public
  code for generating the figures for the PRECISE trial paper

  R

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 8, 2025Apr 8, 2025

• normalbreastDNA

  Public
  R

  •11 fork•44 stars•11 issue•00 pull requests•Updated Feb 17, 2025Feb 17, 2025

• GCC_python_workshop

  Public
  Repository for introduction to RNA seq analysis in python. Workshop hosted by the GCC and led by Reem Elgaish and Ryan Mulqueen.

  Jupyter Notebook

  •11 fork•11 star•00 issues•11 pull request•Updated Feb 10, 2025Feb 10, 2025

• navinlabcode.github.io

  Public
  HTML

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 17, 2025Jan 17, 2025

• vignettes

  Public
  33 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2024Jul 2, 2024

• Arc-well

  Public
  Scripts for the Arc-well paper

  R

  •11 fork•44 stars•00 issues•00 pull requests•Updated Dec 8, 2023Dec 8, 2023

• HumanBreastCellAtlas.github.io

  Public
  The Human Breast Cell Atlas results.

  00 forks•00 stars•66 issues•00 pull requests•Updated Jun 6, 2023Jun 6, 2023

• MissionBio_TNBC_paper

  Public
  Code for the Mission Bio TNBC paper

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 2, 2023Jun 2, 2023

• HumanBreastCellAtlas

  Public
  Repository for codes for the HBCA paper

  R

  •1111 forks•4242 stars•00 issues•00 pull requests•Updated Mar 17, 2023Mar 17, 2023

• CopyKit-UserGuide

  Public
  This is the User Guide for the CopyKit R Package

  TeX

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 8, 2023Feb 8, 2023

• snubar_atac_scripts

  Public
  Scripts (demultiplexing) used in the SNuBar-ATAC manuscript

  Shell

  •00 forks•11 star•11 issue•00 pull requests•Updated Nov 17, 2022Nov 17, 2022

• CNV_pipeline

  Public
  R

  •22 forks•33 stars•00 issues•00 pull requests•Updated Oct 6, 2022Oct 6, 2022

• scquantum

  Public
  R

  •

  GNU General Public License v2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 1, 2022Apr 1, 2022

• CellTrek

  Public
  R

  •2222 forks•129129 stars•2828 issues•00 pull requests•Updated Mar 27, 2022Mar 27, 2022

• PRECISION_clonality_sc

  Public
  Scripts to generate plots used for scDNA precision clonality sample

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 23, 2022Jan 23, 2022

• RcppML

  Public
  Rcpp Machine Learning: Fast robust NMF, divisive clustering, and more

  C++

  •

  GNU General Public License v2.0

  •2121 forks•00 stars•00 issues•00 pull requests•Updated Dec 1, 2021Dec 1, 2021

• ACT_paper

  Public
  Scripts used for the ACT paper

  HTML

  •44 forks•1212 stars•00 issues•00 pull requests•Updated May 6, 2021May 6, 2021

• MVA_CNA

  Public
  Moving average to calculate copy numbers from 10X RNAseq

  R

  •11 fork•22 stars•00 issues•00 pull requests•Updated Nov 12, 2019Nov 12, 2019