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    31 repositories

    • wellDA-seq

      Public
      Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer
      R
      •0•0•0•0•Updated Dec 30, 2025Dec 30, 2025

    • copykit

      Public
      Toolkit for single-cell copy number analysis
      R
      •
      Other
      •4•26•2•0•Updated Dec 15, 2025Dec 15, 2025

    • tnbc-chemo

      Public
      Decoding the Archetypes and Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy
      chemotherapybreast-cancerscrnavisiumtnbcxeniumvisium-hd
      HTML
      •0•3•0•0•Updated Nov 17, 2025Nov 17, 2025

    • copykat

      Public
      R
      •
      Other
      •57•260•66•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•2•0•0•Updated Sep 14, 2025Sep 14, 2025

    • B7-H3

      Public
      R
      •0•0•0•0•Updated Sep 9, 2025Sep 9, 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•40•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
      •21•126•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