Department: Computational Biology
ARIAweb: a server for automated NMR structure calculation
The ARIAweb server provides access to the main ARIA software functionalities (NMR data conversion and structure calculation). In addition, structure calculation results can be easily visualised, with a dedicated molecular viewer and graphical displays […]
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 .
fq2dna (FASTQ files to de novo assembly) is a command line tool to ease the de novo assembly oƒ archaea, bacteria or virus genomes ƒrom raw high-throughput sequencing (HTS) paired-end (PE) reads. Every data […]
ƒqCleanER (ƒastq Cleaning and Enhancing Routine) is a command line tool to ease the diƒƒerent standard preprocessing steps oƒ short high-throughput sequencing (HTS) reads. Eight standard HTS read processing steps can be carried out […]
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 […]
Python-cwlgen is a python library for the generation of CWL programmatically. It supports the generation of CommandLineTool and DockerRequirement. The library works for both Python 2.7.12+ and 3.6.0.
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 […]
sequana_coverage standalone application
sequana_coverage is a standalone application that reports genomic regions of interest (ROIs) which are significantly over- or under-represented in high throughput sequencing data. Thanks to HTML reports, is allows users to browse the detected […]
Shiny Exploration tool for Transcriptomic Analysis