Workflows

What is a Workflow?
15 Workflows visible to you, out of a total of 15
Stable

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MultiAffinity enables the study of how gene dysregulation propagates on a multilayer network on a disease of interest, uncovering key genes. Find the detailed documentation for the tool here.

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Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Mar Batlle

Submitter: Laura Rodriguez-Navas

Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

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Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular interaction ...

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

Work-in-progress

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

Type: Nextflow

Creators: Veit Schwämmle, Magnus Palmblad

Submitters: Laura Rodriguez-Navas, José Mª Fernández

Stable

Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data

Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...

Type: Snakemake

Creators: Ozan Ozisik, Juma Bayjan, Cenna Doornbos, Friederike Ehrhart, Matthias Haimel, Laura Rodriguez-Navas, José Mª Fernández, Eleni Mina, Daniël Wijnbergen

Submitter: Juma Bayjan

Stable

StructuralVariants Workflow

Type: Nextflow

Creators: Laura Rodriguez-Navas, Adrián Muñoz-Civico, Daniel López-López

Submitter: Laura Rodriguez-Navas

Stable

StructuralVariants Workflow

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Daniel López-López

Submitter: Laura Rodriguez-Navas

Stable

Description

The workflow takes an input file with Cancer Driver Genes predictions (i.e. the results provided by a participant), computes a set of metrics, and compares them against the data currently stored in OpenEBench within the TCGA community. Two assessment metrics are provided for that predictions. Also, some plots (which are optional) that allow to visualize the performance of the tool are generated. The workflow consists in three standard steps, defined by OpenEBench. The tools needed ...

Type: Nextflow

Creators: José Mª Fernández, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas

Submitter: Laura Rodriguez-Navas

Stable

Exome SAMtools Workflow

Type: Nextflow

Creator: Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

Stable

Exome Alignment Workflow

Type: Common Workflow Language

Creator: Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

Stable

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...

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