LBMC BioComputing Hub - Blog

Advanced use of git

Club Bioinfo

summary of the training course given by Matthieu Moy in early 2025

An open-source package for the detection of DNA breakpoints with neo-telomere addition

Club Bioinfo

During the past year I have developed a tool for detecting Programmed DNA Elimination (PDE) events, the chopping up and elimination of parts of the genome during early…

A quantitative and predictive computational model of homologous recombination in cells

Club Bioinfo

The supports for this presentation will be available here.

Nicolas Mendiboure

HiC Meta pipeline available

guide

How to use the nextflow HiC meta pipeline

tutorial docker charliecloud

guide

How to build a docker image then charliecloud

Audrey Lapendry

Hub Presentation

git

skills overview

Introduction to {tidymodels} R package

guide

See this presentation from this tutorial¹ by Julie Aubert and Antoine Bichat.

Introduction to ensemble learning

guide

gitbio authentication

git

How to validate your new SSO ENS de Lyon authentication

Stephane Janczarski

R helper packages to develop R packages

guide

gitbio migration

git

How to update your ssh configuration

nf-core

PSMN

nextflow

nf-core

How to run an nf-core pipeline on the PSMN

PSMN migration

PSMN

nextflow

What to do with nextflow and the new PSMN configuration

Quarto: markdown-based document creation/edition

guide

Static website generator and more

Inference and simulation of gene regulatory networks

Club Bioinfo

The rise of single-cell data highlights the need for a nondeterministic view of gene expression, while offering new opportunities regarding gene regulatory network…

JOBIM2022 feedback

Club Bioinfo

presentation.pdf

Audrey Gilbert, Audrey Lapendry, Xavier Grand

git borg linker-core

Club Bioinfo

Incremental backup of your results folder with git and borg

Nicolas Fontrodona

Public Databases

Club Bioinfo

My experience on using public databases (4DN, ENCODE & GEO)

Auredy Lapendry

nf-core

Club Bioinfo

A community effort to collect a curated set of analysis pipelines

Nicolas Fontrodona

Combining R and FIJI to detect and characterize cells on tissue slices

Club Bioinfo

automated detection of cell in slices using R and FIJI

SonarQube

Club Bioinfo

Check the quality of your code with SonarQube

Nicolas Fontrodona

Calibrated Chip-Seq

Club Bioinfo

Nextflow pipeline to process calibrated chip-seq data

The Sphinx and Roxygen2 documentation generators

Club Bioinfo

A documentation generator is a tool that creates software documentation intended for programmers (API documentation), end-users (end-user guide) or both

Nicolas Fontrodona

Nextflow DSL2

Club Bioinfo

changes introduced by the DSL2 of Nextflow

Unit testing with R or Python

Club Bioinfo

Example of unit testing library

Packaging with Python

Club Bioinfo

How to create and share your python package

ChIA-PET

Club Bioinfo

Identifier les interactions de la chromatine grâce à la technologie ChIA-PET

Audrey Lapendry

RNA Direct

Club Bioinfo

Emmanuel Labaronne

Utiliser les ressources de l’IFB

Club Bioinfo

presentation.pdf

GEO Deposit

Club Bioinfo

How to upload your data on GEO

Jean-Baptiste Claude

ACP

Club Bioinfo

DESeq2 usage with R

Hélène Polvech

Random Forest

Club Bioinfo

Simple description and applications

Nicolas Fontrodona

Reproducible science with Docker and VirtualBox

Club Bioinfo

How to use Docker and VirtualBox

ssh & other tools to work remotly

Club Bioinfo

How to work remotly

HBV Transcriptomics

Club Bioinfo

Nanopore long-reads analysis

DESeq2 Model

Club Bioinfo

presentation of the DESeq2 model

DESeq2 R

Club Bioinfo

DESeq2 usage with R

Hélène Polvech

GLM

Club Bioinfo

Generalized Linear Model with R

Claire Burny, Nicolas Fontrodona

Multiple testing

Club Bioinfo

Multiple testing correction

Simple tests

Club Bioinfo

Anissa Guillemin

Linear regression

Club Bioinfo

Linear regression with R