Software

Coded in the lab

VEXOR

Varian/t ExplOreR: Exploratory tool for fine-mapping. VEXOR is a platform-independent browser-based integrative environment for functional annotation in R, based on the Shiny package. This interface provides a comprehensive analytical framework to characterize the role of variants driving susceptibility signals in regions defined by GWAS.

R-Omix: Epigenomics Portal

A portal containing novel bioinformatics tools with highly customizable user interface based on the Shiny framework has been developed by our team. Those interfaces offer the possibility to rapidly generate graphs which are easily integrable in publications. All those bioinformatics tools are closely related to epigenomics fields and are hosted on the Compute Canada‘s infrastructure.

NGS++: C++ library for manipulating Next Generation Sequencing data

Our groups have developed a C++ library designed for Next Generation Sequencing data manipulation. It is specifically tailored to help develop applications that work with genomic regions and features, such as epigenomics marks, gene features and data that are often associated with BED type files.

Bio2RDF: Toward interlinked life science data

The Bio2RDF project uses a data integration approach based on semantic web rules to provide a service to help biologists to understand the mechanisms of life and to better exploit the vast amount of publicly available data.

rGADEM

A package for ChIP-Seq and motif analysis, rGADEM: rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.

rMAT

A package for ChIP-ChIP and tiling arrays, rMAT: This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files.

rTANDEM

A package for Mass spectrometry analysis, rTANDEM (github source): This package interfaces the tandem protein identification algorithm in R.

ShinnyTandem

A package for Mass spectrometry analysis, ShinnyTandem (github source): This package provides a GUI interface for rTANDEM.

Metagene

A Packages for ChIP profiling, metagene (github source): This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features.

Imetagene

A Packages for ChIP profiling, Imetagene (github source): This package provide a graphical user interface to the metagene package. This will allow people with minimal R experience to easily complete metagene analysis.

ENCODExplorer

A Packages for ChIP profiling, ENCODExplorer (github source): This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api.

similaRpeak

A Packages for ChIP profiling, similaRpeak (github source): This package calculates metrics which assign a level of similarity between ChIP-Seq profiles.

nucleoSim

A package for nucleosome positioning, nucleoSim (github source): This package generate synthetic nucleosome maps using parameters given by users. Three different distributions are available: Normal, Student and Uniform.

consensusSeekeR

A package for nucleosome positioning, consensusSeekeR (github source): This package compares genomic positions and genomic ranges from multiple experiments to extract common regions.

RJMCMC

A package for nucleosome positioning, RJMCMC : This package uses informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

ShinySNP

A package for single-nucleotide polymorphisms visualization, ShinySNP: This package provide a highly customizable graphical user interface which enable the visualization of single-nucleotide polymorphisms (SNPs).

methylInheritance

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed. Available here.