Description of EDC bioinformatics tools

All EDC’s projects are available in our GitHub organization https://github.com/parisepigenetics.

Maintained tools

great_3d

A tool for the analysis and visualisation of 3d genome structure, epigenetics and gene expression.
Maintainer : Costas Bouyioukos

ATAC-seq

Jupyter notebooks giving an example of ATAC-seq analysis.
Maintainer : Alix Silvert, Magali Hennion

RASflow_EDC

Workflow for RNA-seq data analysis, based on RASflow which was originally published by X. Zhang. It has been modified to run effectively on both IFB and iPOP-UP core cluster and to fit our specific needs. Moreover, several tools and features were added, including a comprehensive report, as well as the possibility to incorporate the repeats in the analysis. See full documentation.
Maintainer : Magali Hennion

rna_feat_ext

A set of computational tools to extract user defined mRNA features from a list of ENSEMBL gene IDs by using the web API of ENSEMBL BioMart and custom computations.
Maintainer : Costas Bouyioukos

riboproanalysis

RiboProPipe is a pipeline for Ribosome Profiling analysis of any eukaryotic genome from Ensembl 75+ or later. It performs all the necessary pre-processing steps (quality control, filtering, trimming and size selection), filter reads mapped to rRNA, map to reference genome, counting on CDS for each gene and differential analysis from raw Ribosome Profiling data.
Maintainer : Costas Bouyioukos

shiny-your-gene-list

An R-Shiny application for the downstream enrichment analyses of gene lists of interest.
Maintainer : Costas Bouyioukos

pyna-colada

Pyna colada is a python application using ‘straw’ and ‘juice-tools’ to provide a more useful API to work with .hic Hi-C experiments files.
Maintainer : Costas Bouyioukos