Jacques van Helden's repositories
SARS-CoV-2_origins
Analysis of insertions in the genomes and proteins of coronaviruses. Illustration: AvH. (2020). Covid-19 cracked <http://doi.org/10.5281/zenodo.3734643>
statistics-for-bioinformatics
Theory, methods and practicals for the statistical analysis of biological data.
cisreg_course
Course on the analysis of cis-regulatory elements from genomic sequences
stats_avec_RStudio_EBA
Cours “Statistiques avec R" pour l'Ecole de Bioinformatique Aviesan
touret_sars-cov-2_inhibitors
Statistical analysis of Touret's in vitro screening for molecules inhibiting SARS-CoV-2 infection. Illustration: AvH. (2020). Covid-19 cracked (http://doi.org/10.5281/zenodo.3734643).
bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics_course
Support (slides, practicals) for bioinformatics courses by Jacques van Helden
RSAT_Docker
Scripts for creating a Docker container with RSAT
shnc-origines-sars-cov-2
Cours Nature et Culture de la licence Sciences et Humanités, Aix-Marseille Université
statistics_for_bioinformatics
Packages under development, which are used as support to the course "Statistics for bioinformatics" and the accompanying book.
IBIS_2024
Participation to the IBIS nebchmarking for motif discovery approaches
AdventOfCode
Python code for the AdventOfCode challenges
bh2018paris
BioHackathon event website
BioHackathon
Repository with information about the BioHackathon hosted in Paris in Nov 2018
cmb-comp-bio
Computational Biology course of the Master in Computational and Mathematical Biology
Huanan_market_samples_JvH
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC. Analysis built on top of Jesse Bloom's results.
motif_databases
Databases of transcription factor binding motifs for the software suite Regulatory Sequence Analysis Tools (RSAT)
NeAT_ghosts
files that used to be in the RSAT repository, but were only used by NeAT, which is not functional anymore
rna-seq_replicate_analysis
Analysis of the RNA-seq transcriptome data with 48 biological replicates x 7 technical replicates produced by Geoff Barton's lab.
RNAseqMVA_old
Evaluation of multivariate analysis methods for the supervised classification of RNA-seq data
shnc-opsines
Cours Nature & Culture 3 de la licence Sciences et Humanités d'Aix-Marseille Université
snakemake-rsat
some, tentative snakemake workflows developer by Bruno Contreras, Jaime Castro-Mondragon, Claire Rioualen and Jacques van Helden in 2016, not maintained since then.
using_IFB_NNCR
Tutorials for the use of IFB NNCR