Skip to content

index.md

Latest commit

 

History

History
85 lines (53 loc) · 3.44 KB

index.md

File metadata and controls

85 lines (53 loc) · 3.44 KB
layout page
title Introduction
category home
description main page

banner

EDC BiBs core facility

Welcome to the Epigenetics and Cell Fate (UMR7216) Bioinformatics and Biostatistics website.

The UMR7216 BiBs platform provides and develops user-friendly, state of the art epigenomics protocols. We also maintain access to a local computing cluster and provide the teams of the UMR7216 a variety of bioinformatics related services such as technology monitoring, project-specific analyses and user-tailored, on-demand training.

This website is the main resource for protocols, scripts and instructions on how to use the HPC clusters.


How to access the facility

The easiest is to pass by the 329 room in Lamarck A!

You can also contact us by email : bibsATparisepigenetics.com.

If you need long-term help on a specific project, this has to be discussed with BiBs steering committee. Please download and fill-in the accession form (docx or odt) and send it via email. A meeting to discuss your needs will be set-up in the following days.

Our protocols, scripts and workflows are hosted on our GitHub repository. Some of the resources are private, please provide us your GitHub Username to get access.


Stay up to date

In order to get news about bioinformatics in the unit, you can follow us on Slack at hpc-edc.slack.com. To get access, please email us at bibsATparisepigenetics.com.


How can we help you ?

Answer specific questions

Proofreading of grant applications or articles

Literature mining

On-demand training


How can you work on your own?

One important goal of the BiBs facility is to make you able to analyse your data yourself! To do so, we develop easy-to-use workflows and we support community workflows such as the ones from nf-core. We also guide you to use calculation clusters to analyse large datasets.

Using HPC clusters

  1. Getting started on IFB core cluster
  2. Getting started on iPOP-UP cluster
  3. Tips and Tricks

Analysis workflows

  1. RNA-seq by RASflow_EDC
    Implemented by BiBs, this workflow for RNA-seq data analysis is 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.
  2. nf-cores worflows
    Curated set of analysis pipelines built using Nextflow. They can run on both IFB and iPOP-UP clusters.

Steering committee

  • Magali Hennion
  • Florent Hubé
  • Olivier Kirsh
  • Valérie Mezger
  • Jean-François Ouimette
  • Pierre Poulain (Institut Jacques Monod)
  • Claire Rougeulle

Feedback request

This website is currently under construction. We kindly ask our users to provide some feedback about this resource. Please contact us if :

  • something is unclear,
  • you spot some typos,
  • you would like to request topic specific documentation/workflow,
  • you would like to contribute to this resource.