Repositories list

• cutTag-pipeline

  Public
  Pipeline for Cut&Tag analysis

  R

  •

  MIT License

  •7•17•0•0•Updated Jan 16, 2025Jan 16, 2025

• bcl2fastq

  Public
  This repo contains a workflow that takes sequencing output from an Illumina sequencer, uses bcl2fastq to demultiplex reads and convert them to FASTQ format, and runs basic quality control.

  Shell

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• 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

• 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