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    27 repositories

    • CSHL_workshops

      Public
      3•3•0•0•Updated Mar 24, 2025Mar 24, 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

    • copykit

      Public
      Toolkit for single-cell copy number analysis
      R
      •
      Other
      •4•20•3•0•Updated Oct 15, 2024Oct 15, 2024

    • pan_cancer_paper

      Public
      Pan-cancer CNA paper
      R
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • PRECISE_paper

      Public
      code for generating the figures for the PRECISE trial paper
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 31, 2024Aug 31, 2024

    • tnbc-chemo

      Public
      Decoding the Archetypes and Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy
      R
      •0•1•0•0•Updated Aug 28, 2024Aug 28, 2024

    • wellDA-seq

      Public
      Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer
      R
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • vignettes

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

    • copykat

      Public
      R
      •
      Other
      •54•228•57•1•Updated Jun 25, 2024Jun 25, 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
      •10•35•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
      •20•115•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
      •17•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

    • scopit

      Public
      R
      •2•5•0•0•Updated Feb 20, 2019Feb 20, 2019