All Published Workflows

4 workflows that have been reviewed and published

map_metat
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Snakemake workflow to map and quantify metatranscriptomic data using a metagenome reference
public

public

A Snakemake workflow for mapping metatranscriptomic reads against a metagenomic reference. In short, the workflow maps paired...
FASTQ Sample ID Genome assembly Ontology mapping Bowtie 2 edgeR FeatureCounts metagenomeSeq MultiQC Pandas SAMtools Snakemake metagenomics
Free
15
eggnog-functional-annotation-using-snakemake
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Snakemake workflow for functional annotation using eggNOG mapper v2
public

public

Snakemake workflow for automated functional annotation This is a Snakemake workflow for performing functional annotation o...
FASTQ raw sequence reads Annotation Ontology mapping Diamond Snakemake taxonomic and functional annotation
Free
1
rnaseq-pe-main
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RNA-seq paired-end Workflow
public

public

The workflow needs a list of dataset pairs of fastqsanger. As well as a gtf file with genes Optional, but recommen...
FASTQ paired sequencing data Mapping Ontology mapping BEDTools Cufflinks Cutadapt Galaxy MultiQC STAR WorkflowHub RNA-Seq
Free
bridgedb-tutorial-gene-hgnc-name-to-ensembl-identi
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BridgeDb workflow: Gene HGNC name to Ensembl identifier
public

public

This tutorial explains how to use the BridgeDb identifier mapping service to translate HGNC names to Ensembl identifiers. Thi...
JSON Gene identifier Mapping Ontology mapping Pandas ipython matplotlib requests seaborn Data identity and mapping
Free
15