Department: Computational Biology
Sustainable and comprehensive software distribution for the life sciences
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/. […]
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 […]
Comparative Gene Set Enrichment Analysis tool
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.
We have recently developed tools to visualize the results of CRISPR screens and design novel guide RNA for use in bacteria. These tools are available at crispr.pasteur.fr .
Cute Little Functions
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.
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 […]
Linkage Analysis Using TARS
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 […]
Pasteur Galaxy Platform
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 […]
RΕQ: assessing branch supports oƒ a distance-based phylogenetic tree with the rate oƒ elementary quartets
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, […]
Salmonella CRISPR Typing
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 […]
Shiny Exploration tool for Transcriptomic Analysis