All Published Workflows

2 workflows that have been reviewed and published

atac_metacell_utilities
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Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP
public

public

This repository contains a snakemake pipeline for utilities with ATAC and RNA metacells inferred using SEACells algor...
Sample ID Peak calling Gene expression matrix FiMO Pandas SCANPY Snakemake renv numpy scipy SEACells tqdm ChIP-seq
Free
22
scrnaseq-single-sample-processing-starsolo
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scRNAseq Single Sample Processing STARSolo
public

public

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do...
FASTQ paired sequencing data Clustering Gene expression matrix Sample annotation ANN-SoLo Galaxy SCANPY WorkflowHub scRNAseq data processing
Free