Services: Genes And Genomes

a web application that provides a graphical interface for Seurat version 2, a popular single-cell RNA-seq (scRNA-seq) package for R. It provides an easy-to-use UI and the ability to export results as an HTML file.

Prediction of protein sub-mitochondrial localization.

DELLY discovers germline and somatic structural variants in short-read massively parallel sequencing data

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

We provide support and guidance in development of Disease Maps (disease-maps.org), computational and visual repositories of knowledge about mechanisms of human diseases. We offer hosting of open access Disease Maps on the MINERVA Platform (minerva-web.lcsb.uni.lu) on our infrastructure under the elixir-luxembourg.org sub-domain, their backup and conservation. The MINERVA Platform ensures online access, interactive exploration, search for known drug targets and visualisation of omics datasets. We provide training in management of the Disease Maps and guidance to their integration into reproducible computational workflows by using the dedicated API of the hosting platform.

Web interface for assignment and analysis of DNA conformers.

Database Of Local Biomolecumal COnfromers. (Formerly known as DOLCE)

 An API aiming to enable the search of genomic variants and associated information without jeopardising the privacy of the dataset.

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images: it allows users to upload, and download and reprocess the thousands of raw, 2D images used to build a 3D structure.

Produces and maintains automatic and manually curated annotation on eukaryotic genomes. It is integrated with important molecular resources, for example UniProt, and can be accessed programmatically or through a web browser.

Provides annotated genomes of farmed and domesticated animals in an easily viewable format via the Ensembl system.

Provides access to genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces based on the Ensembl software platform.

Enterotypes are densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. Computational methods to detect and characterise enterotypes in any dataset, either to reproduce previous reports or determine enterotypes in new studies, are provided and explained. Part of the Microbiome Analysis Toolbox. 

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Pointers to positions in nucleotide sequence entries provide access to promoter sequences. 

The European Genome-phenome Archive (EGA) allows users to explore datasets from numerous genotype experiments, including case-control, population and family studies, that are supplied by a range of data providers. 

European Variation Archive

The Expression Atlas allows users to search for gene expression changes measured in various cell types, organism parts, and disease states. It represents a curated subset of the ArrayExpress and GEO Archive experiments.

FAIDARE is a portal developed by ELIXIR-FR as an asset of the ELIXIR Plant Science community. FAIDARE enables data discovery through federations of distant Plant informations systems that have set up a standardized Restful API, the BrAPI. FAIDARE currently allows to do detailed searches of accessions and phenotyping data.

This API allows validating JSON contents following JSON Schema defined at https://github.com/fairtracks/fairtracks_standard/

FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.

Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.

A web server for assigning putative cis DNA motifs to input transcription factors (TFs) and conversely for predicting which TFs that might recognize input DNA motifs. 

Web application for the integrative and combined analysis and visualization of multi-level omics data. (Replaced ProMeTra)

An optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.

Prokaryote genome annotation system, modular, flexible and extensible.

Eukaryotic genome annotation system, modular, flexible and extensible.

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

GenExVis (Gene Expression Visualizer) is a desktop application for exploring and visualizing differential gene expression data. 

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).