Workflows

What is a Workflow?
69 Workflows visible to you, out of a total of 69

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

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

This workflow can only work on an experimental setup with exactly 2 conditions. It takes two collections of count tables as input and performs differential expression analysis. Additionally it filters for DE genes based on adjusted p-value and log2 fold changes thresholds. It also generates informative plots.

Type: Galaxy

Creator: Pavankumar Videm

Submitter: WorkflowHub Bot

This workflow is used for GO and KEGG enrichment analysis using GOseq tools.

Type: Galaxy

Creator: Amirhossein Naghsh Nilchi

Submitter: WorkflowHub Bot

Workflow for variant analysis against a reference genome in GenBank format

Type: Galaxy

Creator: Anton Nekrutenko

Submitter: WorkflowHub Bot

No description specified

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

Scaffolding using HiC data with YAHS.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Clinical Metaproteomics 4: Quantitation

Type: Galaxy

Creator: GalaxyP

Submitter: WorkflowHub Bot

Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade

Type: Galaxy

Creators: Peter van Heusden, Peter van Heusden

Submitter: WorkflowHub Bot

This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.

Type: Galaxy

Creators: Wolfgang Maier, Wolfgang Maier

Submitter: WorkflowHub Bot

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