All Published Workflows

4 workflows that have been reviewed and published

pipeline-transcriptome-de
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Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
public

public

This project is deprecated. Please see our newer wf-transcriptomes , which contains functionality for differential exp...
FASTQ Sample ID Alignment Count matrix Minimap2 Quant Salmon SAMtools Snakemake stageR dplyr ggplot2 tidyr Gene expression
Free
14
pyflow-rnaseq
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RNAseq pipeline based on snakemake
public

public

If you use this pipeline, please cite: If inputs are fastq files: The output folder will be suffixed by _fq I...
FASTQ raw sequence reads Filtering Count matrix DeepTools FeatureCounts htseqcount SAMtools Snakemake STAR RNA-Seq
Free
9
fastcn-smk
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A snakemake for fastCN reference setup
public

public

The Snakefile is under workflow . Most installing is done by Snakemake but there is one small Makefile. Please re...
Data Alignment Count matrix rustybam BEDTools mrsFAST Pandas SAMtools seqtk Snakemake fastCN numba pysam Data quality management
Free
33
single_snake_sequencing
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A Snakemake workflow for standardised sc/snRNAseq analysis
public

public

A [Snakemake][sm] workflow for standardised sc/snRNAseq analysis. Find us in the "Standardized Usage" Section of the [Sna...
Sample annotation RNA-Seq analysis Count matrix bcl2fastq-nextseq demultiplexer FastQC MultiQC Pandas SCANPY Snakemake cellranger anndata helpers matplotlib scvi RNA-Seq
Free
21