Workflows

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738 Workflows visible to you, out of a total of 793
EnrichDO: a Global Weighted Model for Disease Ontology Enrichment Analysis

EnrichDO

EnrichDO is a double weighted iterative model by integrating the DO graph topology on a global scale. EnrichDO was based on the latest annotations of the human genome with DO terms, and double weighted the annotated genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between the ...

Type: R markdown

Creators: None

Submitter: Liang Cheng

GALOP - Genome Assembly using Long reads Pipeline
Work-in-progress

GALOP - Genome Assembly using Long reads Pipeline

This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.

At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py and lib/polishing.py files.

galop.py -h 
Mandatory
...

Type: Python

Creators: None

Submitter: Benjamin Istace

rnaseq-de/main

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

Taxonomy classification using Kraken2 and Bracken
Work-in-progress

The aim of this workflow is to handle the routine part of shotgun metagenomics data processing. The workflow is using the tools Kraken2 and Bracken for taxonomy classification and the KrakenTools to evaluate diversity metrics. This workflow was tested on Galaxy Australia. A How-to guide for the workflow can be found at: https://github.com/vmurigneu/kraken_howto_ga_workflows

Type: Galaxy

Creators: Valentine Murigneux, QCIF/Biocommons, mike thang

Submitter: Valentine Murigneux

cfDNA UniFlow: A unified preprocessing pipeline for cell-free DNA data from liquid biopsies
Stable

cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...

Type: Snakemake

Creator: Sebastian Röner

Submitter: Sebastian Röner

DOI: 10.48546/workflowhub.workflow.1091.2

goseq/main

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

Type: Galaxy

Creator: Amirhossein Naghsh Nilchi

Submitter: WorkflowHub Bot

Multiomic ALS signatures highlight sex differences and molecular subclusters and identify the MAPK pathway as therapeutic target
Stable

This repository contains the analytical pipeline for the MAXOMOD project, which focuses on the multi-omic analysis of axono-synaptic degeneration in the motor neuron disease amyotrophic lateral sclerosis (ALS). The project explores sex differences and molecular subclusters in ALS and investigates the MAPK pathway as a potential therapeutic target.

For a detailed understanding of the scientific background and the findings, refer to our paper published on [Nature ...

Type: DVC

Creator: Fabian Hausmann

Submitter: Fabian Hausmann

DOI: 10.48546/workflowhub.workflow.1191.1

AMR-Pathfinder
Work-in-progress

This is an aggregation of the work done in Seq4AMR consisting of the following workflows:

Installation

  • You will need to:
  • run the [RGI Database ...

Type: Galaxy

Creators: Helena Rasche, Dennis Dollée, Birgit Rijvers

Submitter: Helena Rasche

DOI: 10.48546/workflowhub.workflow.1189.1

The Polygenic Score Catalog Calculator
Stable

The Polygenic Score Catalog Calculator (pgsc_calc)

Documentation Status pgscatalog/pgsc_calc CI DOI ...

Type: Nextflow

Creators: Samuel Lambert, Benjamin Wingfield, Laurent Gil

Submitter: Samuel Lambert

haploid-variant-calling-wgs-pe/main

Workflow for variant analysis against a reference genome in GenBank format

Type: Galaxy

Creator: Anton Nekrutenko

Submitter: WorkflowHub Bot

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