Metabolism Python Packages

cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

52K 588 242

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

4K 15 9

brendapyrser

A Python parser for the BRENDA database

4K 34 11

reframed

ReFramed: metabolic modeling package

1K 63 15

carveme

CarveMe: genome-scale metabolic model reconstruction

1K 223 69

sccellfie

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

729 64 4

biosimulators-masspy

MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

397 1 0

scmeta

A python library for single-cell metabolism data analysis.

390 21 5

efmlrs

Python package and workflow for EFM calculation via (mp)lrs and efmtool

386 6 1

miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

338 12 2

cellmetpro

Analyse cellular metabolic states of cells from scRNA-seq data using FBA and Genome-scale Metabolic Models

311 0 0

framed

framed: a metabolic modeling package for python

288 25 10

corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

249 27 8

gmcspy

Efficient calculation of gMCS in python.

238 6 1

findcpcli

findCP CLI package - find ChokePoint reactions in genome-scale metabolic models

198 3 0

biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

181 1 0

nutramilo-nis

Open-source algorithm for estimating the relative insulinogenic potential of meals from nutritional composition.

163 0 0

multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

140 9 3

contrabass

Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es

137 3 1

biocatalyzer

BioCatalyzer: a rule-based tool to predict compound metabolism

118 7 0

pygenprop

A python library for programmatic usage of EBI InterPro Genome Properties.

110 9 5

fasting

A Python package to interact with fasting logs from apps like Zero.

96 10 1

ggshu

Multi-dimensional, trans-omics metabolic maps.

95 56 1

designmc

Designing microbial communities

51 8 4