Service list

A transcriptome-based breast tumor diagnostic tool

A database annotating organellar RNA editing processes in their biological context.

A database of RNA editing events in humans from RNA-Seq and DNA-Seq data.

Python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

Redundans is a pipeline that assists the assembly of heterozygous genomes. It takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly. 

ReferenceSeeker determines closely-related reference genomes following a scalable hierarchical approach. It combines a fast kmer profile-based database lookup of candidate reference genomes and subsequent computation of specific average nucleotide identity (ANI) values.

Tools to analyse cis-regulatory elements in genome sequences

ReMap is a manually curated knowledge base of transcriptional regulatory binding, built on standardized data processing and large-scale integrative analysis of DNA-binding data.

Set of tools and a web server for complex characterization of repetitive DNA based on data from next generation of sequence reads.

A database of annotated tandem repeat protein structures, combining computer-based methods and manual curation.

The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.

A tool that can be used to manage researchers’ access rights to bioinformatics databases.

REXdb: a reference database of transposable element protein domains

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

rGreat is an R package which acts as a client of GREAT enrichment analysis analysis

The rhdf5 and Rhdf5lib packages combine to provide an interface between HDF5 and R. The HDF5 file format provides the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) in a completely portable manner. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
In particular HDF5 is being used to address the rapid growth in the size of single-cell datasets, and rhdf5 is a cornerstone to many existing analysis tools.

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. 

A web portal dedicated to ribosome profiling (RiboSeq) data analysis. There are currently two resources with Tutorial support and a Forum for both.

Residue interaction network generator. RING identifies all types of non-covalent interactions at atomic level in a protein structure (PDB);

RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.

Providing access to many NGS and RNA tools, visualisations, interactive environments (e.g. IPython) as well as various utilities, reference genomes and data libraries.

End-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. Starting from the FASTQ files are aligned to the reference genome, and a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample is prepared. Performance of exploratory data analysis (EDA) for quality assessment and exploration of the relationship between samples, performance of differential gene expression analysis, and visual exploration of the results.

RnBeads is an R package for analysing DNA methylation data obtained with an experimental protocol that provides single-CpG resolution. 

Identification and validation of predictive biomarkers based on gene expression in solid tumors

Roddy is a framework for large scale NGS processing pipelines on Petabyte scale. It is used for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Web tool for prediction of rRNA secondary structures.

Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. The tools can be accessed via a Web site (http:rsat.eu/), as Web services, or installed locally on Linux / Mac OS X systems.

A framework for software development in bioinformatics. It covers three aspects:.

1. Workflow wrapping the TF text-mining results from https://github.com/fnl plus other databases. 
2. High Throughput Sequencing related functionalities.
3. Rbbt wrapper for the Variant Effect Predictor.

Auto-downloads and installs the software.

Web interface accessing a curated database with information about biochemical reactions and kinetic properties in an experimental or environmental context.

A comprehensive data resource for salmonids species based on different omics data