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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.

58K 560 233
mjenior
riptide

Reaction Inclusion by Parsimony and Transcript Distribution

5K 13 7
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.

2K 61 4
cdanielmachado
carveme

CarveMe: genome-scale metabolic model reconstruction

2K 204 64
SCMeTA
scmeta

A python library for single-cell metabolism data analysis.

788 20 5
biosimulators
biosimulators-masspy

BioSimulators-compliant command-line interface to the MassPY simulation program <https://masspy.readthedocs.io/>.

632 1 0
cdiener
corda

Genome-scale model construction with CORDA

592 25 8
cdanielmachado
framed

framed: a metabolic modeling package for python

574 26 10
BeeAnka
efmlrs

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

514 6 1
robaina
brendapyrser

Tools to parse the BRENDA database

462 33 10
MetExplore
miom

Mixed Integer Optimization for Metabolism

360 12 2
biosimulations
biosimulations-bigg

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

345 1 0
findCP
findcpcli

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

327 3 0
openCONTRABASS
contrabass

Constraint-based model vulnerabilities analysis

244 3 1
omicspilot
cellmetpro

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

225 0 0
Micromeda
pygenprop

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

200 9 5
jcorreia11
biocatalyzer

BioCatalyzer: a rule-based tool to predict compound metabolism

177 7 0
PlanesLab
gmcspy

Efficient calculation of gMCS in python.

175 6 1
biosustain
multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

169 9 3
jbpauly
fasting

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

147 10 1
biosustain
ggshu

Grammar of Graphics for shu.

133 54 1
cdanielmachado
designmc

Designing microbial communities

88 8 4
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