Workflows

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10 Workflows visible to you, out of a total of 13
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 ...

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 ...

Stable

COnSensus Interaction Network InFErence Service

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

alt text

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 ...

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

Stable

VIRify

VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs. VIRify was implemented in CWL. What do I need? The ...

Type: Nextflow

Creators: Martin Beracochea, Martin Hölzer, Alexandre Almeida, Guillermo Rangel-Pineros and Ekaterina Sakharova

Submitter: Laura Rodriguez-Navas

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