Workflows

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1461 Workflows visible to you, out of a total of 1556
vvv2_align_PE_bwamem2
Stable

Using:

  • vadr annotation (virus model must be selected in options)
  • vardict variant caller
  • coverage depth Provides summarizing files:
  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)
  • vcf file with significant variants only [optional in command line tool vvv2_display]

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

Apache Airflow Classical Molecular Interaction Potentials
Stable

CMIP tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), ...

Type: Apache Airflow

Creators: Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.2157.1

CWL Classical Molecular Interaction Potentials
Stable

CMIP tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), ...

Type: Common Workflow Language

Creators: Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.2156.1

Gene EXpansion and CONtraction analysis pipeline
Stable

EXCON (v2.1.1)

A Nextflow pipeline for gene family EXpansion and CONtraction analysis across multiple species using CAFE5.

Given a set of genome assemblies and annotations, EXCON builds orthogroups with OrthoFinder, fits and compares multiple CAFE models to identify gene families evolving at significantly different rates, and automatically selects the best-fitting model for downstream analysis. Optionally, GO enrichment analysis can be run on expanded and contracted gene families, and ...

Type: Nextflow

Creator: Christopher Wyatt

Submitter: Chris Wyatt

DOI: 10.48546/workflowhub.workflow.2141.5

GLEAM Multimodal Learner - HANCOCK recurrence prediction

Train and evaluate a HANCOCK recurrence model with Multimodal Learner

Associated Tutorial

This workflows is part of the tutorial Gleam Multimodal Learner - Head and Neck cancer Recurrence Prediction with HANCOCK, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

Apache Airflow GMX Automatic Ligand Parameterization tutorial
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Type: Apache Airflow

Creators: Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.2120.1

X-omics iPSC project analysis workflow

iPSC Data Analysis

Description

This project is part of the Dutch X-omics initiative and focuses on the analysis of multi-omics data from several iPSC lines. The data included genomics, transcriptomics, proteomics, and several different types of metabolomics.

Goal

The goal is to identify disease-specific traits of the patient-derived iPSC compared to various control lines.

Pipeline overview

File outline

|- README.md     # This readme\ |- Data analysis plan.md ...

Type: Nextflow

Creator: Casper de Visser

Submitter: Casper de Visser

DOI: 10.48546/workflowhub.workflow.2154.1

EATRIS-Plus Multi-omics Analysis Workflow

EATRIS-Plus Multi-omics Analysis Workflow

Analysis workflow used to analyze the cohort of healthy blood donors

Prerequisites

Multi-omics data set from Zenodo

Install Nextflow using conda

Create a Conda Environment:

conda create -n nextflow-env 
conda activate nextflow-env 
conda install -c bioconda
...

Type: Nextflow

Creator: Casper de Visser

Submitter: Casper de Visser

DOI: 10.48546/workflowhub.workflow.2153.1

CPSM: Survival Risk Modeling Workflow Using Transcriptomics and Clinical Data
Stable

CPSM: Cancer patient survival model - Workflow

Introduction

CPSM is an R package that provides a comprehensive computational pipeline for predicting survival probabilities and risk groups in cancer patients. It includes dedicated modules to perform key steps such as data preprocessing, training/test splitting, and normalization. CPSM enables feature selection through univariate cox-regression survival analysis, feature selection though LASSO method, and calculates a LASSO-based Prognostic ...

Type: R Markdown document

Creators: Harpreet Kaur, Pijush Das, Kevin Camphausen, Uma Shankavaram

Submitter: Harpreet Kaur

DOI: 10.48546/workflowhub.workflow.2129.1

Apache Airflow Protein-Membrane MD analysis tutorial
Stable

Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the ...

Type: Apache Airflow

Creators: Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.2152.1

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