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10k_genomes

Various scripts for efficient processing of 10k Salmonella genomes

acidify-me

A ME-model framework to simulate the response of E. coli under acid stress

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.

ai_in_actuarial_science

Code accompanying the paper "AI in Actuarial Science"

amp_pub

Files associated with the ampir paper

arboreto

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

atlas

ATLAS - Three commands to start analysing your metagenome data

autodl

Solution for AutoDL challenge

automated-feature-engineering

Automated feature engineering in Python with Featuretools

autopacmen

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

avian-immunity

Scripts for studying the evolution of immune genes across birds.

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-deep-learning-single-cell-papers

aybrah

Analyzing Yeasts by Reconstructing Ancestry of Homologs

bgwas

R package to perform Bayesian Genome-Wide Association Studies

bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

biopandas

Working with molecular structures in pandas DataFrames

biopycourse

Python short course for graduates in biology and biochemistry

biostructmap

A Python package for mapping sequence aligned data onto protein structures

books

cameo

cameo - computer aided metabolic engineering & optimization

candida-albicans-microbiome-interaction

caret

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models

carvefungi

carveme

CarveMe: genome-scale metabolic model reconstruction

cellfactory-ecyeastgem

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.

chemprop

Message Passing Neural Networks for Molecule Property Prediction

childrengutmicrobialgems

58 GEMs for gut bacterial species from microbiota of healthy and malnourished children.

cinderella

Causal Inference Networks for Determining Expression Relationships Anthology

cnnc

covolutional neural network based coexpression analysis