Workflows

What is a Workflow?
169 Workflows visible to you, out of a total of 169

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

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

Type: Nextflow

Creators: Austyn Trull, Lara Ianov

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

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

Type: Galaxy

Creators: Abromics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

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