maxsonBraunLab

gopeaks

Peak caller for CUT&TAG data

cutTag-pipeline

Pipeline for Cut&Tag analysis

CITEViz

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

atac_seq

process and analyze paired-end ATAC-Seq data

cite_seq

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

gopeaks-compare

Compare CUT&TAG peak callers

hint-atac-old

find transcription factor footprints with ATAC-Seq

cuttag---old

Tools for CUT&RUN and CUT&Tag analyses

Bulk-RNA-seq-pipeline-PE

Bulk-RNA-seq-pipeline-SE

Analyze single-end RNA-Seq data

chip_seq

process and analyze paired-end ChIP-Seq data

atac_seq---old

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

callpeaks

DEPRECATED - Custom peak caller for CUT&TAG data

ChIP-seq-pipeline-----old

Chromatin immunoprecipitation sequencing analysis pipeline.

ChIPseq-pipeline

MaxsonLab ChIP seq pipeline

CITEViz-CRAN-version

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

CITEVizTestData

ExperimentHub package for PBMC CITE-Seq datasets

cutAnd_seacr---old

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

cutAndQC---old

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

rna_seq

RNA-Seq pipeline for bulk, paired-end data

scRNA-Seq

Analyze 10X Chromium data for several samples

scRNA_sample

Example scRNAseq processing

slurm

SLURM profile for maxsonBraunLab pipelines

snakemake_setup

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