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Type: Organization
Type: Organization
process and analyze paired-end ATAC-Seq data
This is a pipeline for the beginning analysis of paired end ATAC seq data
Analyze single-end RNA-Seq data
DEPRECATED - Custom peak caller for CUT&TAG data
Chromatin immunoprecipitation sequencing analysis pipeline.
process and analyze paired-end ChIP-Seq data
MaxsonLab ChIP seq pipeline
Process CITE-Seq data using Seurat. Steps include pre-processing, sample clustering, sample integration, and group clustering.
CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq
CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq. Forked for CRAN formatting. Currently under construction.
ExperimentHub package for PBMC CITE-Seq datasets
Input: fastq or bams; Output: bedgraphs, seacr peaks, counts table
Snakemake QC pipeline for Cut&Tag / Cut&Run experiments
Tools for CUT&RUN and CUT&Tag analyses
Pipeline for Cut&Tag analysis
Peak caller for CUT&TAG data
Compare CUT&TAG peak callers
find transcription factor footprints with ATAC-Seq
RNA-Seq pipeline for bulk, paired-end data
Analyze 10X Chromium data for several samples
Example scRNAseq processing
SLURM profile for maxsonBraunLab pipelines
This repo is for setting up a Snakemake environment for maxsonBraunLab pipelines.
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