Repositories list

• scPrinter

  Public
  Python

  •

  MIT License

  •1•21•0•0•Updated Feb 6, 2025Feb 6, 2025

• PRINT

  Public
  Jupyter Notebook

  •1•8•0•0•Updated Feb 5, 2025Feb 5, 2025

• exigs_code

  Public
  Code to process and analyze ExIGS data from Labade*, Chiang*, Comenho* et al.

  MATLAB

  •

  MIT License

  •0•1•0•0•Updated Sep 24, 2024Sep 24, 2024

• FigR

  Public
  Functional Inference of Gene Regulation

  HTML

  •

  MIT License

  •10•39•26•1•Updated Jul 5, 2024Jul 5, 2024

• GMP_analyses_code

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Feb 13, 2024Feb 13, 2024

• stimATAC_analyses_code

  Public
  All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs

  R

  •12•38•1•1•Updated Mar 20, 2023Mar 20, 2023

• buenrostrolab.github.io

  Public
  Buenrostro Lab Webpage Repo

  HTML

  •

  MIT License

  •17k•1•0•0•Updated Mar 28, 2022Mar 28, 2022

• slide_dna_seq_analysis

  Public
  Analysis of slide-DNA-seq data in Zhao, Chiang, et al.

  MATLAB

  •1•4•1•0•Updated Oct 6, 2021Oct 6, 2021

• lungATAC_analysis_code

  Public
  R

  •1•1•0•0•Updated May 17, 2020May 17, 2020

• 10x_multibead_images

  Public
  Repo for images for 10X imaging

  0•0•0•0•Updated Oct 3, 2019Oct 3, 2019

• dscATAC_analysis_code

  Public
  Analysis repository for "Droplet-based combinatorial indexing for massive scale single-cell epigenomics"

  R

  •3•10•1•0•Updated Sep 30, 2019Sep 30, 2019

• immgen_atac_rna_data

  Public
  Repository that pairs the ImmGen ATAC and RNA data (Yoshida et al 2019 Cell)

  0•0•0•0•Updated May 9, 2019May 9, 2019

• proatac

  Public
  Preprocessing pipeline for (sc)ATAC data

  Python

  •

  MIT License

  •2•0•0•0•Updated Dec 4, 2018Dec 4, 2018

• bap

  Public
  Bead single-cell atac processing

  Python

  •

  MIT License

  •8•0•0•0•Updated Oct 30, 2018Oct 30, 2018

• singlecell_bloodtraits

  Public
  Data/analysis repository for "Interrogation of human hematopoiesis..." paper

  R

  •10•0•0•0•Updated Oct 28, 2018Oct 28, 2018

• biorad_scRNAseq

  Public
  CL Analysis of BioRad scRNA-seq data

  R

  •0•0•0•0•Updated Aug 26, 2018Aug 26, 2018

• tss-annotation

  Public
  Simple reproducible managment of annotated TSS and gene bodies

  Shell

  •1•4•0•0•Updated Jun 7, 2018Jun 7, 2018

• chromVARmotifs

  Public
  R package with motifs for use with chromVAR

  R

  •

  Other

  •9•1•0•0•Updated Nov 16, 2017Nov 16, 2017

• chromVARguide

  Public
  Repo for walking through a chromVAR sample analysis

  HTML

  •1•2•0•0•Updated Aug 8, 2017Aug 8, 2017

• differential_expression_example

  Public
  Sample repo for running DESeq2 on HTSeq (counts)

  0•0•0•0•Updated Jul 8, 2017Jul 8, 2017

• PEAT

  Public
  An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.

  C++

  •

  Other

  •7•0•0•0•Updated Jun 13, 2017Jun 13, 2017

• mitoblacklist

  Public
  Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome

  Shell

  •7•1•0•0•Updated Jun 12, 2017Jun 12, 2017

• easyLift

  Public
  R package for easy mm9 <-> mm10 / hg19 <-> hg38

  R

  •

  MIT License

  •2•1•0•0•Updated May 21, 2017May 21, 2017

• indrops_sm

  Public
  07March Runs at first

  R

  •0•0•1•0•Updated May 7, 2017May 7, 2017

• labknowledge

  Public
  Institutional Knowledge, Tips, & Tricks

  HTML

  •0•0•0•0•Updated Apr 22, 2017Apr 22, 2017

• ImmGen

  Public
  Analyses pertaining to ImmGen

  HTML

  •

  MIT License

  •0•0•0•0•Updated Feb 17, 2017Feb 17, 2017

• kmercor

  Public
  Mouse kmer corr

  HTML

  •0•0•0•0•Updated Feb 5, 2017Feb 5, 2017

• inferCNV

  Public
  Inferring CNV from Single-Cell RNA-Seq

  R

  •170•1•0•0•Updated Jan 23, 2017Jan 23, 2017

• ImmGen_amit

  Public
  Repository for code/data for mouse heme RNA/ATAC/ChIP-Seq

  R

  •0•1•0•0•Updated Jan 15, 2017Jan 15, 2017

• cellrangerRkit

  Public
  v1.1.0

  R

  •2•4•0•0•Updated Jan 6, 2017Jan 6, 2017