Service list

VarAFT is a software designed to annotate and filter Human NGS data. This system was developed within the RD-Connect project and was instrumental for the creation of the RD-Connect Genome-Phenome platform. As a stand-alone java system, it ensures full data protection, critical for clinical use. VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples can be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique variant priorization features including OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP . It is used by many research and clinical laboratories worldwide.

Performs ranking of variants in genomic datasets, integrating information from multiple sources to prioritize each variant by its deleteriousness, novelty and existing information.

Accurate validation, mapping and formatting of sequence variant descriptions

A high recall search engine to support the curation of genomic variants.

https://academic.oup.com/bioinformatics/article/38/9/2595/6547047

VEuPathDB provides access to diverse genomic and other large scale datasets related to eukaryotic pathogens and invertebrate disease vectors.

Galaxy server for the functional annotation and prioritization of genetic variants.

A resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries. 

WarPP is a fully automated procedure to place water molecules in the active site of a protein structure. 

A web-accessible, single cell RNA-Seq processing platform designed for the management, analysis and interpretation of scRNA-seq high-throughput data.

Atlas of Protein Hydration

A software package for the automatic discovery of enriched motifs in a set of related DNA sequences, including ChIP-Seq peaks.

WESkit is an open source implementation of a Workflow Execution Service (WES). It tries to be GA4GH-compliant.

WheatIS is a portal that enables data discovery through an international federation of distant informations systems about wheat genetics and genomics in the frame of the Wheat Initiative (www.wheatinitiative.org). The WheatIS portal allows a keyword-based discovery of any type of data. It currently gives a single entry point to data provided by twelve different worldwide institutes.

An open, collaborative platform dedicated to the curation of biological pathways

Federated genomics data sharing platform allowing users to query genomic and phenotypic information.

Workflow Execution Service automating a number of steps, including: 

1. Fetch and cache a workflow a number of sources
2. Identify the kind of workflow.
3. Fetch and set up workflow execution engine
4. Identify the needed containers by the workflow
5. Execute the workflow in a secure way

Workflow plugins provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).

Workflow plugins provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).

Workflow4Metabolomics resource is based on the Galaxy environment that provides user-friendly interfaces to build, run, and share comprehensive data analysis workflows and gives access to a High Performance Computing environment the ELIXIR-FR/IFB infrastructure. Thus, W4M offers more than 40 tools to process data from all three main technologies (NMR, GCMS, LCMS), including unique algorithms developed by the W4M developers themselves. Data and workflows can be re-used and publicly shared, thus becoming useful references for the community. Finally, the platform provides many tutorials and a help desk.

A registry for describing, sharing and publishing scientific computational workflows. WorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. This is achieved through extensive use of open standards and tools, including Common Workflow Language (CWL), RO-Crate, BioSchemas and Tool Registry Service (TRS)

This package provides functions and routines for a supervised analysis of somatic signatures. In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

YEASTRACT is a curated repository of approximately 175.000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae.