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    37 repositories

    • scPrinter

      Public
      Jupyter Notebook
      •
      MIT License
      •11•72•12•0•Updated May 7, 2026May 7, 2026

    • PRINT

      Public
      Jupyter Notebook
      •6•26•0•0•Updated Dec 10, 2025Dec 10, 2025

    • exigs_code

      Public
      Code to process and analyze ExIGS data from Labade*, Chiang*, Comenho* et al.
      MATLAB
      •
      MIT License
      •0•2•0•0•Updated May 7, 2025May 7, 2025

    • FigR

      Public
      Functional Inference of Gene Regulation
      HTML
      •
      MIT License
      •12•53•26•2•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
      •13•41•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•2•0•Updated Oct 6, 2021Oct 6, 2021

    • lungATAC_analysis_code

      Public
      R
      •1•3•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•11•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
      •8•2•0•0•Updated Jun 12, 2017Jun 12, 2017

    • easyLift

      Public
      R package for easy mm9 <-> mm10 / hg19 <-> hg38
      R
      •
      MIT License
      •2•2•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
      •179•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
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