etienne loire's repositories
vcf2DIYABC.py
script that convert vcf file into genotype data matrix to input DIYABC program.
CCS_RNAseq_analysis
Dataset and analysis of albopictus expression profiles following infection with dengue or RVF viruses
formation_python
support de cours de anne muriel chifolleau
IntregrativeHealthConcept
Datasets and analysis of integrative health bibliography
paceup_nanopore_WGS_AMR
snakemake pipeline dedicated to analysis of WGS analysis of resistant bacteria
Abomsa_scripts
Scripts used in the Abomsa Paper.
amblyoma_paper
script, data and figures for the amblyoma paper
AMR_mada2020
collection of scripts, pipeline and data used to analyze transmission of ESBL-Ec strains in madagascar
bac2ass
Create assembly from BAC short read sequences
blasr
BLASR: The PacBio® long read aligner
BTVsequencing
Script and Data for BTV WGS experiment
dilectus_pumillo_dufour
scripts to analyse claire dataset
dotsfiles
my dot files (bashrc, vimrc, tmux.conf, and whatnot)
galapagos_reveal.js
presentation based on reveal.js + shiny + plot_ly
GalapagosData_And_Script
Data and script used to produce the Figure 1 of the Chelonoidis Nigra 2016 paper
IT_PGM_CMAEE_pipeline
pipeline using various tools to treat ion-torrent PGM tool
MatSupp_Moreau20JVir
Supplementary material for the article "The genome segments of Bluetongue virus differ in copy number in a host-specific manner" by Moreau et al
Moubata_paper
scripts and data used for the moubata paper
PPRanalysis
script and data for PPR viral analysis
roumagnac2018_figs
data, script and figures for the minion/illumina comparison of viral sequencing
SeekViralReads
short pipeline designed to run on the CIRAD cluster. Allow the detection of viral sequences in fastq file.
SILVI
a pipeline to facilitate in T-cell epitope selection
snakevirome
snakemake pipeline for metavirome assembly and analysis
svm-r-markdown-templates
I have a suite of R Markdown templates for academic manuscripts, beamer presentations, and syllabi. I share them here.
Varhap
pipeline for snp detection in haploid sequence