Bioinformatics and Biostatistics HUB

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. Life science uses many different formats. They may be old, or with complex syntax and converting […]

Cocaine addiction (CocAdd) is a major public health issue affecting 3% of the worlwide population, without validated pharmacotherapy. Nicotinic acetylcholine receptors (nAChRs)have been repeatedly associated in Human and rodent response to cocaine. nAChRs alpha5 […]

The cornerstone of the ELIXIR Tools platform is the bio.tools ELIXIR Tools and Data Services Registry, a discovery portal for a wide range of key bioinformatics resources, which is developed through ELIXIR-EXCELERATE Work Package […]

Drug resistance mutations (DRM) emerge in HIV-1 viruses through selective pressure during antiviral treatment (ART). Acquired drug resistance rates vary depending on duration of ART and type of prescribed regimen. Drug resistance can then […]

Project context and summary : The phylogenetic position and status of “giant viruses”, formerly called NucleoCytoplasmic Large DNA viruses (NCLDV) or putative order Megavirales, are controversial. Many preliminary phylogenetic analyses have been published, but […]

Bioweb is a web portal to search and access the bioinformatics resources available at the Institut Pasteur. It provides an overview of the resources available in the central infrastructure, as well as features to identify […]

In the context of the Swiss consortium InfectX (www.infectx.ch), we have previously performed siRNA, microRNA and drug screens  to investigate signaling pathways modulating invasion of host cells by the bacterial pathogen Listeria monocytogenes. In […]

Listeriolysin S is a bacteriocin specifically produced in the intestine of orally infected mice and necessary for Listeria monocytogenes survival in this organ. In order to investigate whether this toxin might influence the composition […]

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Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]

The pathogenesis of HIV infection, and in particular the development of immunodeficiency, remains incompletely understood. During HIV infection both innate and adaptive immune responses are raised, but they appear to be insufficient or too […]

The PIBnet initiative is a large collaborative program that aims at reinforcing microbial strain collection management and characterization approaches and technologies. It involves National Reference Centers, WHO-collaborative centers, biological resources centers and other microbiological expertise laboratories, together […]

To perform the assembly of a bacterial genome from Illumina sequencing in order to submit it to the MicroScope/MaGe platform of Genoscope.

Hydrogen Deuterium eXchange followed by Mass Spectrometry (HDX-MS) is a recognized biophysical tool in structural biology capable of probing protein/ligand interactions, conformational changes, and protein folding and dynamics. The use of improved HDX-MS workflows […]

To perform assignment of 16S sequences to bacterial genera and statistical analysis of variations of bacterial populations collected from mice feces

The goal of this project is to set sequence analysis tools to evaluate the frequency of mutations within a pool of bacteriophage genomes sequenced by NGS.

JolyTree is a script that implements an alignment-ƒree distance-based procedure ƒor inferring phylogenetic trees ƒrom genome contig sequences. For each pair of genomes, a dissimilarity measure is ƒirst computed and next transƒormed to obtain […]

BACNET is a Java based platform to develop website for multi-omics analysis. Our platform integrates different type of tools, the three most important being: A table tools for Heatmap drawing and manipulation. Genome viewer […]

JASS is a python package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface. The generation of joint […]

Goalign and Gotree are comand line tools aiming at manipulating multiple alignments and phylogenetic trees. They are implemented in Go language. Goalign aims at handling multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, […]

Free, simple to use web service dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.

CRAW is a package which aim to compute and visualize the coverage of RNA seq experiments. The main feature of this tools is the coverage is computed on the both strands, and is centred […]

Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format. listeriomics.pasteur.fr The main purpose of the website is […]

Sequana is a Python framework designed to provide pipelines to analyse Next Generation Sequencing data sets. Sequana provides tools to access the sequence quality but also post-processing analysis such as depth of coverage or […]

BioServices is a Python package that provides access to many Bioinformatics Web Services (e.g., UniProt, KEGG, NCBI) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols). The primary […]

SynTView is a comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic […]

DREAMTools aims at sharing code used in the scoring of DREAMchallenges that pose fundamental questions about system biology and translational medicine. For more information please visit the following links Source code: github.com/dreamtools Documentation: http://dreamtools.readthedocs.io

GDSCTools is a free open-source Python library dedicated to the study of drug responses in the context of the GDSC (Genomics of Drug Sensitivity in Cancer) project. The main developer is `Thomas Cokelaer (Institut […]

This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of […]

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 […]

SHAMAN is a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, […]

Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except […]

RΕQ is a program ƒor quickly estimating a conƒidence value at each branch oƒ a distance-based phylogenetic tree. Branch support assessment is commonly based on bootstrap procedures (e.g. Felsenstein 1985, Makarenkov et al. 2010, […]

Shiny Exploration tool for Transcriptomic Analysis

Comparative Gene Set Enrichment Analysis tool

Sustainable and comprehensive software distribution for the life sciences

This project aims at efficiently storing millions of unique molecular compounds along with some of their already calculated properties. The database named Chem-REST is able to deal with extensive sets of data: millions of […]

The EDAM Browser is a client-side web-based visualization javascript widget for the navigation of the EDAM ontology. EDAM is a structured and controlled vocabulary describing bioinformatics and computational biology concepts. It is used to […]

Integrated bash and R toolbox for linkage analysis using SLURM (TARS Cluster) that include (1) basic quality control of initial file structures, (2) quality control analysis and file preparation by the Alohomora software and […]

Cute Little Functions contains 16 functions for R/RStudio that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.

Comat is a R toolbox that provides quality control reports, matrix distances, permutation test, corrected p values and graphics for the 2 by 2 comparison of contingency matrices of same dimension in batches.

CRISPR polymorphism is a powerful tool to subtype Salmonella strains and is now used in routine for epidemiological investigations. This tool gets a CRISPR profile by identifying the presence of known spacers and direct […]

ToolDog is a program that generates tool description from a tool entry from https://bio.tools.

checkMyIndex is an application whose goal is to help in finding a set of compatible indexes for a sequencing experiment. It has been developped using the R/Shiny environment and is freely available at https://checkmyindex.pasteur.fr/. […]

In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary […]

Galaxy is an open source, web-based platform for data intensive biomedical research. It is developed by the Galaxy Team, which is based at the part of the Center for Comparative Genomics and Bioinformatics at […]