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maxsonbraunlab's Projects

atac_seq icon atac_seq

process and analyze paired-end ATAC-Seq data

atac_seq---old icon atac_seq---old

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

callpeaks icon callpeaks

DEPRECATED - Custom peak caller for CUT&TAG data

chip_seq icon chip_seq

process and analyze paired-end ChIP-Seq data

cite_seq icon cite_seq

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

citeviz icon citeviz

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

citeviz-cran-version icon citeviz-cran-version

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

rna_seq icon rna_seq

RNA-Seq pipeline for bulk, paired-end data

scrna-seq icon scrna-seq

Analyze 10X Chromium data for several samples

slurm icon slurm

SLURM profile for maxsonBraunLab pipelines

snakemake_setup icon snakemake_setup

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

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