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Metabolism Python Packages

Python packages with the GitHub topic metabolism. Sorted by relevance, with stars and monthly downloads.
opencobra
cobra

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

59K 560 234
mjenior
riptide

Reaction Inclusion by Parsimony and Transcript Distribution

8K 13 7
cdanielmachado
carveme

CarveMe: genome-scale metabolic model reconstruction

2K 203 63
cdanielmachado
reframed

ReFramed: metabolic modeling package

2K 63 15
earmingol
sccellfie

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

1K 57 3
cdanielmachado
framed

framed: a metabolic modeling package for python

949 26 10
SCMeTA
scmeta

A python library for single-cell metabolism data analysis.

673 20 5
MetExplore
miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

579 12 2
BeeAnka
efmlrs

Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that have been compressed with EFMlrs

558 6 1
robaina
brendapyrser

A Python parser for the BRENDA database

541 33 10
biosimulators
biosimulators-masspy

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

541 1 0
cdiener
corda

Genome-scale model construction with CORDA

527 25 8
findCP
findcpcli

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

324 3 0
biosimulations
biosimulations-bigg

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

279 1 0
Micromeda
pygenprop

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

245 9 5
PlanesLab
gmcspy

gMCSpy is a python package for the calculation of Genetic Minimal Cut sets (GMCS). In simple terms, the idea is to take a metabolic model and calculate the genetic vulnerabilities that will render the biomass production impossible. This is done through a Mixed-Integer Linear problem (MILP) formulation and the use of a linear solver.

210 6 1
openCONTRABASS
contrabass

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

171 3 1
biosustain
multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

166 9 3
omicspilot
cellmetpro

Cellular Metabolic Profiler - Analyze and visualize metabolic profiles from scRNA-seq data

165 0 0
biosustain
ggshu

Grammar of Graphics for shu.

158 54 1
jcorreia11
biocatalyzer

BioCatalyzer: a rule-based tool to predict compound metabolism

148 7 0
jbpauly
fasting

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

126 10 1
cdanielmachado
designmc

Designing microbial communities

85 8 4
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