Repositories list

• scRNA-Seq

  Public
  Analyze 10X Chromium data for several samples

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• chip_seq

  Public
  process and analyze paired-end ChIP-Seq data

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• Bulk-RNA-seq-pipeline-SE

  Public
  Analyze single-end RNA-Seq data

  R

  •

  MIT License

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• cite_seq

  Public
  Process CITE-Seq data using Seurat. Steps include pre-processing, sample clustering, sample integration, and group clustering.

  Python

  •0•3•0•0•Updated Dec 18, 2024Dec 18, 2024

• atac_seq

  Public
  process and analyze paired-end ATAC-Seq data

  chip-seqatac-seqngs-analysis+ 2ngs-pipelinepipeline

  R

  •1•3•0•0•Updated Dec 18, 2024Dec 18, 2024

• cutTag-pipeline

  Public
  Pipeline for Cut&Tag analysis

  R

  •

  MIT License

  •7•17•0•0•Updated Dec 18, 2024Dec 18, 2024

• Bulk-RNA-seq-pipeline-PE

  Public
  R

  •3•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• rna_seq

  Public
  RNA-Seq pipeline for bulk, paired-end data

  R

  •

  MIT License

  •0•2•0•0•Updated Dec 18, 2024Dec 18, 2024

• CITEViz

  Public
  CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq

  r-shinyscrna-seqflow-cytometry+ 2multi-omicssingle-cell

  R

  •

  MIT License

  •5•6•3•1•Updated Jun 6, 2024Jun 6, 2024

• snakemake_setup

  Public
  This repo is for setting up a Snakemake environment for maxsonBraunLab pipelines.

  MIT License

  •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

• CITEVizTestData

  Public
  ExperimentHub package for PBMC CITE-Seq datasets

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 6, 2023Feb 6, 2023

• slurm

  Public
  SLURM profile for maxsonBraunLab pipelines

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 30, 2022Nov 30, 2022

• CITEViz-CRAN-version

  Public
  CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq. Forked for CRAN formatting. Currently under construction.

  R

  •

  Other

  •5•0•0•0•Updated Oct 27, 2022Oct 27, 2022

• gopeaks

  Public
  Peak caller for CUT&TAG data

  Go

  •

  MIT License

  •1•25•3•0•Updated Aug 18, 2022Aug 18, 2022

• gopeaks-compare

  Public
  Compare CUT&TAG peak callers

  R

  •

  MIT License

  •2•2•0•0•Updated Apr 15, 2022Apr 15, 2022

• callpeaks

  Public
  DEPRECATED - Custom peak caller for CUT&TAG data

  Python

  •2•0•0•0•Updated Apr 26, 2021Apr 26, 2021

• ChIPseq-pipeline

  Public
  MaxsonLab ChIP seq pipeline

  0•0•0•0•Updated Mar 13, 2021Mar 13, 2021

• ChIP-seq-pipeline-----old

  Public
  Chromatin immunoprecipitation sequencing analysis pipeline.

  Python

  •2•0•0•0•Updated Feb 17, 2021Feb 17, 2021

• scRNA_sample

  Public
  Example scRNAseq processing

  HTML

  •0•0•0•0•Updated Feb 3, 2021Feb 3, 2021

• hint-atac-old

  Public
  find transcription factor footprints with ATAC-Seq

  Python

  •0•3•0•0•Updated Feb 2, 2021Feb 2, 2021

• atac_seq---old

  Public
  This is a pipeline for the beginning analysis of paired end ATAC seq data

  Python

  •0•0•0•0•Updated Sep 4, 2020Sep 4, 2020

• cutAnd_seacr---old

  Public
  Input: fastq or bams; Output: bedgraphs, seacr peaks, counts table

  Shell

  •2•0•0•0•Updated Jul 21, 2020Jul 21, 2020

• cutAndQC---old

  Public
  Snakemake QC pipeline for Cut&Tag / Cut&Run experiments

  Python

  •0•0•0•0•Updated Jun 17, 2020Jun 17, 2020

• cuttag---old

  Public
  Tools for CUT&RUN and CUT&Tag analyses

  Shell

  •

  GNU General Public License v3.0

  •2•1•0•0•Updated Jan 29, 2020Jan 29, 2020