Repositories list

• tnbc-chemo

  Public
  Decoding the Archetypes and Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy

  chemotherapybreast-cancerscrna+ 4visiumtnbcxeniumvisium-hd

  HTML

  •0•2•0•0•Updated Oct 31, 2025Oct 31, 2025

• copykat

  Public
  R

  •

  Other

  •57•257•64•1•Updated Oct 13, 2025Oct 13, 2025

• DCIS_TME

  Public
  R

  •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

• wellDR-seq

  Public
  Code deposit for wellDR-seq paper

  R

  •2•1•0•0•Updated Sep 14, 2025Sep 14, 2025

• B7-H3

  Public
  R

  •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

• wellDA-seq

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

  R

  •0•0•0•0•Updated Jul 19, 2025Jul 19, 2025

• copykit

  Public
  Toolkit for single-cell copy number analysis

  R

  •

  Other

  •5•24•4•0•Updated Jul 11, 2025Jul 11, 2025

• CSHL_workshops

  Public
  3•6•0•0•Updated May 1, 2025May 1, 2025

• intro_bioinfo_course

  Public
  introduction to bioinformatics workshop

  HTML

  •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025

• PRECISE_paper

  Public
  code for generating the figures for the PRECISE trial paper

  R

  •

  MIT License

  •0•1•0•0•Updated Apr 8, 2025Apr 8, 2025

• normalbreastDNA

  Public
  R

  •1•4•1•0•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

  •1•1•0•1•Updated Feb 10, 2025Feb 10, 2025

• navinlabcode.github.io

  Public
  HTML

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• pan_cancer_paper

  Public
  Pan-cancer CNA paper

  R

  •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

• vignettes

  Public
  3•0•0•0•Updated Jul 2, 2024Jul 2, 2024

• Arc-well

  Public
  Scripts for the Arc-well paper

  R

  •1•3•0•0•Updated Dec 8, 2023Dec 8, 2023

• HumanBreastCellAtlas.github.io

  Public
  The Human Breast Cell Atlas results.

  0•0•6•0•Updated Jun 6, 2023Jun 6, 2023

• MissionBio_TNBC_paper

  Public
  Code for the Mission Bio TNBC paper

  R

  •0•0•0•0•Updated Jun 2, 2023Jun 2, 2023

• HumanBreastCellAtlas

  Public
  Repository for codes for the HBCA paper

  R

  •11•38•0•0•Updated Mar 17, 2023Mar 17, 2023

• CopyKit-UserGuide

  Public
  This is the User Guide for the CopyKit R Package

  TeX

  •0•2•0•0•Updated Feb 8, 2023Feb 8, 2023

• snubar_atac_scripts

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

  Shell

  •0•1•1•0•Updated Nov 17, 2022Nov 17, 2022

• CNV_pipeline

  Public
  R

  •2•2•0•0•Updated Oct 6, 2022Oct 6, 2022

• scquantum

  Public
  R

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Apr 1, 2022Apr 1, 2022

• CellTrek

  Public
  R

  •22•125•28•0•Updated Mar 27, 2022Mar 27, 2022

• CopyKit_paper

  Public
  Scripts to reproduce the figures from the CopyKit manuscript

  HTML

  •

  MIT License

  •0•0•0•0•Updated Mar 11, 2022Mar 11, 2022

• PRECISION_clonality_sc

  Public
  Scripts to generate plots used for scDNA precision clonality sample

  R

  •1•0•0•0•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

  •18•0•0•0•Updated Dec 1, 2021Dec 1, 2021

• ACT_paper

  Public
  Scripts used for the ACT paper

  HTML

  •4•12•0•0•Updated May 6, 2021May 6, 2021

• MVA_CNA

  Public
  Moving average to calculate copy numbers from 10X RNAseq

  R

  •1•2•0•0•Updated Nov 12, 2019Nov 12, 2019

• pmultinom

  Public
  R

  •0•0•0•0•Updated Sep 20, 2019Sep 20, 2019