nigiord

SFBIStats

Data and charts related to the recent french bioinformatics job market.

ipython_extensions

My IPython extensions

adv-r

Advanced R: a book

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

BioinfoSummerSchoolAngers2018

Jupyter notebook for the Environmental Genomics session at the Angers Bioinfo Summer School 2018

carveme

CarveMe: genome-scale metabolic model reconstruction

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

conky

Light-weight system monitor for X.

cv

Personal Curriculum Vitae

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

Extended_abstract_MTNS

Sources of an extended abstract written for the MTNS2014 conference

micom

Python package to study microbial communities using metabolic modeling.

MicrobeCensus

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data

mountyzilla

MountyZilla, une extension Firefox pour le jeu MountyHall

odes

git repo of the odes scikit for scipy

pandoc_resume

The Markdown Resume

pelican-themes

Themes for pelican

Practical_Exercices_ENS_Cobrapy

The tex and requirement files for a TP on Flux Balance Analysis using Cobrapy given at the École Normale Supérieure (Imalis graduate program) on October, 21th 2014.

presto

Presto performs a fast Wilcoxon rank sum test and auROC analysis. Latest benchmark ran 1 million observations, 1K features, and 10 groups in 16 seconds (sparse input) and 85 seconds (dense input).

Prodigal

Prodigal Gene Prediction Software

ReMapEnrich

ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

Reserve_parlementaire

Quick analysis of the allocation of the French "réserve parlementaire" in 2015

SALib

Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods.

seurat

R toolkit for single cell genomics

seurat-object

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

thesis_manuscript_microbial_growth_control_changing_environment

This is the sources of my PhD thesis titled: "Microbial growth control in changing environments"

tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

webpage-giordano

Source files used to generate my personal website using Pelican

wellFARE

Python package for fluorescent reporter data analysis