Repositories list

• navinlabcode.github.io

  Public
  HTML

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• copykit

  Public
  Toolkit for single-cell copy number analysis

  R

  •

  Other

  •4•18•3•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•0•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•214•54•1•Updated Jun 25, 2024Jun 25, 2024

• ESO

  Public
  R

  •0•0•0•0•Updated May 18, 2024May 18, 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•108•27•0•Updated Mar 27, 2022Mar 27, 2022

• CopyKit_paper

  Public
  Scripts to reproduce the figures from the CopyKit manuscript

  HTML

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  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