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    27 repositories

    • 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.
      0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • navinlabcode.github.io

      Public
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • copykit

      Public
      Toolkit for single-cell copy number analysis
      R
      •
      Other
      •4•18•4•0•Updated Oct 15, 2024Oct 15, 2024

    • normalbreastDNA

      Public
      R
      •1•3•0•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
      2•0•0•0•Updated Jul 2, 2024Jul 2, 2024

    • CSHL_workshops

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

    • copykat

      Public
      R
      •
      Other
      •55•216•54•1•Updated Jun 25, 2024Jun 25, 2024

    • Arc-well

      Public
      Scripts for the Arc-well paper
      R
      •1•2•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•1•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
      •19•109•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
      •16•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