mgalardini

pyseer

SEER, reimplemented in python 🐍🔮

python_plotting_snippets

Tips and tricks for plotting in python

pdb2uniprot

Convert PDB residues to their Uniprot equivalents

chembl_tools

Small scripts to make the most of the ChEMBL API

2017_python_course

Intermediate python programming course 🐍🏫

abstractFFT

"Abstract" paintings using Fourier transform tricks 🎨🖥️

2016_python_course

Material for the EBI predocs course on python

2018_ecoli_pathogenicity

Highlight genetic determinants of E. coli's pathogenicity

pangenome_variation

Run several analysis on bacterial genomes

ecopredict

Code for growth phenotypes prediction in E. coli and manuscript figures generation

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

reads2transcriptome

From second generation sequencing reads to base counts

2018koyeast

Analysis of multiple yeast strains whole-genome knockout libraries 🔬📈

2019_ecoli_trascriptome

Analysis of E. coli transcriptomics data 📝📊

2021_python_course

2022_ecoli_commensal

Bacterial wg-GWAS for the detection of E. coli BSI and commensal genetic determinants

bioconda-recipes

Conda recipes for the bioconda channel.

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

dpu

Data Processing Unit for eVOLVER

evolver-electron

genomeDCA

glmnet_python

Iris

Iris: expanding the palette of microbial phenotypic readouts

loq

talk to type

mastodon_digest

A Python script that aggregates recent popular tweets from your Mastodon timeline

panaroo

An updated pipeline for pangenome investigation

project-template

Template for a computational project using python, snakemake and jupyter notebooks

Roary

Rapid large-scale prokaryote pan genome analysis

screenings

Chemical genetic data analysis pipeline

seer_pipeline

Run SEER with fewer headaches