Workflows

What is a Workflow?
816 Workflows visible to you, out of a total of 890
clinicalmp-data-interpretation/main

This workflow will perform taxonomic and functional annotations using Unipept and statistical analysis using MSstatsTMT.

Type: Galaxy

Creator: GalaxyP

Submitter: WorkflowHub Bot

clinicalmp-verification/main

In proteomics research, verifying detected peptides is essential for ensuring data accuracy and biological relevance. This tutorial continues from the clinical metaproteomics discovery workflow, focusing on verifying identified microbial peptides using the PepQuery tool.

Type: Galaxy

Creator: Pratik Jagtap

Submitter: WorkflowHub Bot

nf-core/metapep

From metagenomes to peptides

Type: Nextflow

Creators: Sabrina Krakau, Leon Kuchenbecker and Till Englert

Submitter: WorkflowHub Bot

clinicalmp-database-generation/main

The workflow begins with the Database Generation process. The Galaxy-P team has developed a workflow that collects protein sequences from known disease-causing microorganisms to build a comprehensive database. This extensive database is then refined into a smaller, more relevant dataset using the Metanovo tool.

Type: Galaxy

Creator: Subina Mehta

Submitter: WorkflowHub Bot

Test at SC24
No description specified

Type: COMPSs

Creator: Daniele Lezzi

Submitter: Daniele Lezzi

Ecoregionalization workflow (Part 2)

Second part of the ecoregionalization

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Type: Galaxy

Creator: Pauline Seguineau

Submitter: Pauline Seguineau

DOI: 10.48546/workflowhub.workflow.1209.1

Ecoregionalization workflow (Part 1)

Part 1 of ecoregionalization workflow

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Type: Galaxy

Creator: Pauline Seguineau

Submitter: Pauline Seguineau

DOI: 10.48546/workflowhub.workflow.1208.1

Fgenesh annotation -TSI

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

Inputs required: assembled-genome.fasta, hard-repeat-masked-genome.fasta, and (because this workflow maps known mRNA ...

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.5

pseudobulk-worflow-decoupler-edger/main

This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.

Type: Galaxy

Creators: Diana Chiang Jurado, Pavankumar Videm, Pablo Moreno

Submitter: WorkflowHub Bot

Proximity interactomes of human PRICKLE1, PRICKLE2 and PRICKLE3.

KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Armed with PRICKLE(3)s: Stabilizing WNT/PCP complexes against RNF43-mediated ubiquitination". Workflow was built using the KNIME software container environment, version 4.7.7a, which can be created using "docker pull cfprot/knime:4.7.7a" command in Docker. The input data for the KNIME workflow (the report.tsv from DIA-NN) can be found on PRIDE repository under the identifier PXD057854.

Type: KNIME

Creators: Kristina Gomoryova, David Potěšil

Submitter: Kristina Gomoryova

DOI: 10.48546/workflowhub.workflow.1202.1

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