Structure Content

ABSD is a database containing antibody sequences sourced from various repositories such as the PDB, GeneBank, IMGT, UniProt, INN, among others.Despite the abundance of possible antibody sequences, only a few thousand human sequences are publicly accessible as of […]

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 .

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 […]

EXOTICS (EXplOre sysTems omICS) is a shiny app to perform functional enrichment analysis of bulk transcriptomic data at the gene-set level to complement gene-level analyses. The classical transcriptomics analysis consists of differential expression analysis, […]

Cytokinesis leads to the physical separation of daughter cells and concludes cell division. Final abscission occurs close to the midbody (or Flemming body), a prominent structure that matures at the center of the intercellular […]

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 […]

HARIBOSS is a database of RNA-small molecules structures retrieved from the PDB database. HARIBOSS is regularly updated with all the structures resolved by X-ray, NMR, and cryo-EM, in which ligands with drug-like properties interact […]

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 […]

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 […]

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 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, […]

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 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

To help scientists and bioinformaticians to be autonomous to deploy their R/Python shiny [1] application on the web, we developed toolkit named Shiny-K8s [2] that leverage Docker [3] to containerize the application in a […]

The single cell transcriptomics, epigenetic and genomics are supported by collaborative effort of the CB UTechS, Biomics and the Hub. The CB UTechS gathers expertise and high-end instrumentation for single cell phenotyping and sorting, single cell […]

Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification […]

The Spirochase website is an easy-to-navigate portal to all reference proteomes within the Spirochaetes phylum. Here, proteins are organized into orthologous groups (OGs), each with a unique identifier and annotation. With Spirochase, you can […]