ArnaudBelcour

scikit-learn

scikit-learn: machine learning in Python

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

runner

The Runner for GitHub Actions :rocket:

biopandas

Working with molecular structures in pandas DataFrames

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

pdbfixer

PDBFixer fixes problems in PDB files

Prodigal

Prodigal Gene Prediction Software

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

miniprot

Align proteins to genomes with splicing and frameshift

funannotate

Eukaryotic Genome Annotation Pipeline

interproscan

Genome-scale protein function classification

bioservices

Access to Biological Web Services from Python.

panaroo

An updated pipeline for pangenome investigation

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

inStrain

Bioinformatics program inStrain

RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

yeast-GEM

The consensus GEM for Saccharomyces cerevisiae

biom-format

The Biological Observation Matrix (BIOM) Format Project

micom

Python package to study microbial communities using metabolic modeling.

guide

🦮 An introduction to our Answer Set Programming tools focusing on gringo, clingo, and clasp.

ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

Unipressed

Comprehensive Python client for the Uniprot REST API

AGORA

The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.

reconstructor

This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and benchmarking scores for reconstructor models. Reconstructor is a COBRApy compatible, automated GENRE building tool from gene fastas based on KEGG annotations.

meneco

:m: Metabolic network completion

GR

Genome Research template for LaTeX

FunctionalPrediction5000species

Code for paper Weber Zendrera, Sokolovska, Soula. Functional prediction of environmental variablesusing metabolic networks. Scientific Reports (2021)

aucomana