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pypi.org "biology" keyword

View the packages on the pypi.org package registry that are tagged with the "biology" keyword.

Top 2.0% on pypi.org
multiqc 1.27.1
Create aggregate bioinformatics analysis reports across many samples and tools
52 versions - Latest release: 9 months ago - 7 dependent packages - 74 dependent repositories - 46.8 thousand downloads last month - 1,162 stars on GitHub - 1 maintainer
Top 1.6% on pypi.org
biothings-client 0.4.1
Python Client for BioThings API services.
13 versions - Latest release: 10 months ago - 6 dependent packages - 74 dependent repositories - 979 thousand downloads last month - 18 stars on GitHub - 2 maintainers
ifpd 2.1.1
An iFISH probe design pipeline, with web interface included.
21 versions - Latest release: almost 4 years ago - 1 dependent repositories - 47 downloads last month - 12 stars on GitHub - 1 maintainer
dnaweaver 0.3.10
Make ordering and assembly plans for DNA sequences
11 versions - Latest release: 6 months ago - 1 dependent repositories - 262 downloads last month - 28 stars on GitHub - 1 maintainer
phenopype 6.1.0
A phenotyping pipeline for python
54 versions - Latest release: 9 months ago - 1 dependent package - 1 dependent repositories - 64 downloads last month - 12 stars on GitHub - 1 maintainer
methurator 0.1.0
Package for sequencing saturation analysis of sequencing methylation data.
1 version - Latest release: about 15 hours ago
cellsepi 1.1.9
Segmentation of microscopy images and data analysis pipeline with a graphical user interface, pow...
25 versions - Latest release: about 1 month ago - 195 downloads last month - 1 stars on GitHub - 4 maintainers
Top 3.1% on pypi.org
opentrons 8.7.0
The Opentrons API is a simple framework designed to make writing automated biology lab protocols ...
395 versions - Latest release: about 1 month ago - 3 dependent packages - 29 dependent repositories - 42.8 thousand downloads last month - 474 stars on GitHub - 1 maintainer
Top 4.2% on pypi.org
opentrons-shared-data 8.7.0
A bundle of data and python binding that supports the Opentrons API.Does not need to be installed...
334 versions - Latest release: about 1 month ago - 2 dependent packages - 8 dependent repositories - 42.4 thousand downloads last month - 474 stars on GitHub - 1 maintainer
umite 0.1.0
UMI counting tool for SmartSeq3 libraries
1 version - Latest release: about 19 hours ago - 1 maintainer
pyprot 0.1-alpha
Python Proteins
1 version - Latest release: over 8 years ago - 1 dependent repositories - 6 downloads last month - 9 stars on GitHub - 1 maintainer
flugibson 1.2 💰
A Python package for designing influenza reverse genetics primers using the seam...
3 versions - Latest release: over 10 years ago - 1 dependent repositories - 19 downloads last month - 1 stars on GitHub - 1 maintainer
cenfind 0.15.2
Score cells for centrioles in IF data
35 versions - Latest release: about 1 year ago - 191 downloads last month - 1 stars on GitHub - 2 maintainers
escher-legacy 1.7.4
Escher-legacy: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of...
1 version - Latest release: almost 3 years ago - 1 dependent package - 16 downloads last month - 222 stars on GitHub - 1 maintainer
splitp 0.3.2 💰
Phylogenetic tools and methods involving splits and matrix rank
9 versions - Latest release: 5 months ago - 1 dependent repositories - 41 downloads last month - 1 stars on GitHub - 1 maintainer
gilda-slim 1.4.1
Grounding for biomedical entities with contextual disambiguation
3 versions - Latest release: about 2 months ago - 795 downloads last month - 45 stars on GitHub - 1 maintainer
bauble 1.0.62
Ghini is a biodiversity collection manager software application
11 versions - Latest release: about 9 years ago - 3 dependent repositories - 100 downloads last month - 25 stars on GitHub - 1 maintainer
Top 1.7% on pypi.org
dendropy 5.0.8
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...
30 versions - Latest release: 5 months ago - 33 dependent packages - 109 dependent repositories - 93.4 thousand downloads last month - 202 stars on GitHub - 3 maintainers
snptools 0.01
A suite of tools for use in SNP research
1 version - Latest release: about 2 years ago - 2 dependent repositories - 1 maintainer
cellprofiler-core-nightly 5.0.0.dev306
cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
38 versions - Latest release: 1 day ago - 1 dependent package - 291 downloads last month - 1,051 stars on GitHub - 2 maintainers
cellprofiler-nightly 5.0.0.dev306
CellProfiler is a free open-source software designed to enable biologists without training in com...
38 versions - Latest release: 1 day ago - 213 downloads last month - 1,033 stars on GitHub - 2 maintainers
cellprofiler-library-nightly 5.0.0.dev306
cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usa...
38 versions - Latest release: 1 day ago - 2 dependent packages - 282 downloads last month - 1,033 stars on GitHub - 2 maintainers
bioino 0.0.2
Lightweight IO and conversion for bioinformatics file formats.
4 versions - Latest release: over 1 year ago - 1 dependent package - 898 downloads last month - 1 stars on GitHub - 1 maintainer
rainbow-optical-flow 2022.4.6
Automated air liquid interface cell culture analysis using deep optical flow.
1 version - Latest release: over 3 years ago - 1 dependent repositories - 12 downloads last month - 4 stars on GitHub - 1 maintainer
dspp-keras 0.0.5
Integration of Database of structural propensities of proteins (dSPP) with Keras Machine Learning...
5 versions - Latest release: over 8 years ago - 1 dependent repositories - 27 downloads last month - 166 stars on GitHub - 1 maintainer
helical 1.4.10
Helical Python SDK
42 versions - Latest release: 2 days ago - 1.08 thousand downloads last month - 153 stars on GitHub - 2 maintainers
sci-phy 0.1.0
Sci-Phy is a python package for the statistical analysis and modelling of evolved data using phy...
1 version - Latest release: about 4 years ago - 1 dependent repositories - 11 downloads last month - 1 maintainer
basicpy 1.2.0
A python package for background and shading correction of optical microscopy images
8 versions - Latest release: over 1 year ago - 2 dependent packages - 1 dependent repositories - 4.59 thousand downloads last month - 86 stars on GitHub - 3 maintainers
pbalancing 2.1.5
Parameter Balancing for Kinetic Metabolic Models
50 versions - Latest release: almost 5 years ago - 1 dependent repositories - 66 downloads last month - 2 maintainers
Top 6.9% on pypi.org
cogent3 2025.9.8a9
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems ...
63 versions - Latest release: 2 days ago - 5 dependent packages - 5 dependent repositories - 14.3 thousand downloads last month - 131 stars on GitHub - 3 maintainers
omics_pipe 1.1.3
A Computational Framework for Reproducible Multi-Omics Data Analysis
2 versions - Latest release: about 2 years ago - 2 dependent repositories - 4 downloads last month - 1 maintainer
pioreactor 25.11.12
The core Python app of the Pioreactor. Control your bioreactor through Python.
127 versions - Latest release: 2 days ago - 1 dependent repositories - 419 downloads last month - 97 stars on GitHub - 1 maintainer
impy 0.2.8
Integrated Metaomic Pipeline command-line utility.
13 versions - Latest release: over 8 years ago - 1 dependent repositories - 175 downloads last month - 1 maintainer
afscgap 2.0.2
Tools for interacting with the public bottom trawl surveys data from the NOAA AFSC GAP.
17 versions - Latest release: 13 days ago - 2 dependent repositories - 462 downloads last month - 5 stars on GitHub - 1 maintainer
wc-sim 0.0.1
Sequential whole-cell model simulator
1 version - Latest release: about 2 years ago - 1 dependent repositories - 6 stars on GitHub - 2 maintainers
pinetree 0.5.0
stochastic simulation of gene expression with site-specific translation rates
9 versions - Latest release: 4 months ago - 1 dependent repositories - 30 downloads last month - 12 stars on GitHub - 3 maintainers
pydisconet 0.2.0
analyzing the co-authorship network of researchers in the field of biology
2 versions - Latest release: about 1 year ago - 34 downloads last month - 0 stars on GitHub - 1 maintainer
Top 3.3% on pypi.org
pytdc 1.1.15
Therapeutics Commons
72 versions - Latest release: 8 months ago - 5 dependent packages - 12 dependent repositories - 60.7 thousand downloads last month - 930 stars on GitHub - 3 maintainers
cocopye 0.5.0
Feature-based prediction of genome quality indices
12 versions - Latest release: over 1 year ago - 58 downloads last month - 2 stars on GitHub - 1 maintainer
methscan 1.1.0
a command line tool for Single-Cell Analysis of Methylation data
4 versions - Latest release: about 1 year ago - 57 downloads last month - 14 stars on GitHub - 1 maintainer
physcraper 1.0.0
Physcraper
7 versions - Latest release: about 4 years ago - 1 dependent repositories - 30 downloads last month - 13 stars on GitHub - 1 maintainer
actonet 1.0
Abduction-based control of Boolean networks fixpoints
2 versions - Latest release: over 5 years ago - 46 downloads last month - 1 maintainer
Top 7.2% on pypi.org
gilda 1.4.1
Grounding for biomedical entities with contextual disambiguation
22 versions - Latest release: 6 months ago - 8 dependent packages - 12 dependent repositories - 17.2 thousand downloads last month - 45 stars on GitHub - 1 maintainer
moldrug 3.7.3
moldrug is a python package for drug-oriented optimization on the chemical space.
35 versions - Latest release: over 1 year ago - 1 dependent repositories - 180 downloads last month - 37 stars on GitHub - 1 maintainer
flexidot 2.0.2
Flexible dotplotting of genomic sequences.
3 versions - Latest release: 5 days ago - 22 downloads last month - 92 stars on GitHub - 2 maintainers
biobear 0.23.7 💰
A package for working with Bioinformatics data with SQL and Arrow
67 versions - Latest release: 10 months ago - 1 dependent package - 8.16 thousand downloads last month - 190 stars on GitHub - 1 maintainer
mummichog 2.7.0
Pathway and network analysis for metabolomics data
13 versions - Latest release: over 1 year ago - 1 dependent repositories - 74 downloads last month - 42 stars on GitHub - 1 maintainer
structural 3.1.1
A module for a wide variety of methods that permit access to the constraint information in the st...
11 versions - Latest release: over 7 years ago - 54 dependent repositories - 58 downloads last month - 3 stars on GitHub - 2 maintainers
partsdb 0.2.0
Database of genetic parts
3 versions - Latest release: over 8 years ago - 2 dependent repositories - 13 downloads last month - 4 stars on GitHub - 1 maintainer
proteingraphml 0.1.1
Knowledge Graphs for Protein Science
2 versions - Latest release: about 4 years ago - 1 dependent repositories - 9 downloads last month - 20 stars on GitHub - 1 maintainer
lib310-lite 0.1.1
lib310 Lite Python Package
52 versions - Latest release: over 2 years ago - 103 downloads last month - 2 maintainers
sinetra 0.1.5
Generate synthetic data for biological particle tracking
6 versions - Latest release: about 1 month ago - 40 downloads last month - 8 stars on GitHub - 1 maintainer
bones 0.1
A python toolkit for biology
1 version - Latest release: about 2 years ago - 2 dependent repositories - 1 maintainer
open-af3 0.0.8 💰
Paper - Pytorch
1 version - Latest release: 5 months ago - 12 downloads last month - 792 stars on GitHub - 1 maintainer
pyscuba 0.1.1
Python for Single-cell Clustering Using Bifurcation Analysis
2 versions - Latest release: over 9 years ago - 1 dependent repositories - 12 downloads last month - 0 stars on GitHub - 1 maintainer
emmaa 1.17.0
Ecosystem of Machine-maintained Models with Automated Analysis
15 versions - Latest release: over 4 years ago - 1 dependent repositories - 72 downloads last month - 11 stars on GitHub - 1 maintainer
genochain 0.0.7
Storing and versioning genomics data on a blockchain
2 versions - Latest release: over 2 years ago - 17 downloads last month - 1 maintainer
kvasirhgt 0.6.7
A package to identify HGT in bacterial genomes
5 versions - Latest release: over 8 years ago - 1 dependent repositories - 14 downloads last month - 10 stars on GitHub - 1 maintainer
topkappy 0.2.4
Pythonic wrapper for the Kappa language (bio simulations)
6 versions - Latest release: about 5 years ago - 1 dependent repositories - 26 downloads last month - 5 stars on GitHub - 1 maintainer
pygenomes 0.1.0
a command-line tool for downloading genome data from UCSC ftp site.
1 version - Latest release: over 10 years ago - 2 dependent repositories - 8 downloads last month - 1 maintainer
Top 10.0% on pypi.org
valerius 0.2.0
Biological sequence analysis tools.
2 versions - Latest release: about 7 years ago - 4 dependent repositories - 7.73 thousand downloads last month - 1 maintainer
zeigen 0.3.0
Find water networks in atomic-resolution crystal structures
12 versions - Latest release: about 3 years ago - 1 dependent repositories - 22 downloads last month - 0 stars on GitHub - 1 maintainer
sid 0.2.5
Image processing for seed images
6 versions - Latest release: almost 6 years ago - 1 dependent repositories - 280 downloads last month - 1 stars on GitHub - 1 maintainer
streq 0.0.2
Basic utilities for working with nucleotide sequence strings.
2 versions - Latest release: over 2 years ago - 3 dependent packages - 1 dependent repositories - 49 downloads last month - 0 stars on GitHub - 1 maintainer
pydiopt 0.1.2
pyDIOPT - Python Wrapper for DIOPT
3 versions - Latest release: over 1 year ago - 35 downloads last month - 0 stars on GitHub - 1 maintainer
cabean 1.0
Python interface to CABEAN, A Software Tool for the Control of Asynchronous Boolean Networks
2 versions - Latest release: over 5 years ago - 26 downloads last month - 2 stars on GitHub - 1 maintainer
spliceai-pytorch 0.0.4
SpliceAI - Pytorch
4 versions - Latest release: over 2 years ago - 17 downloads last month - 14 stars on GitHub - 1 maintainer
kimya 0.0.4
A Simple-to-Use Module About Science.
4 versions - Latest release: almost 3 years ago - 13 downloads last month - 1 maintainer
biology-files 0.3.4
Save and load common biology file formats
10 versions - Latest release: 8 days ago - 807 downloads last month - 1 stars on GitHub - 1 maintainer
pandora-bio 0.2.2
pandora, a collection of handy functions.
1 version - Latest release: 12 months ago - 10 downloads last month - 0 stars on GitHub - 1 maintainer
metquest 0.1.34
MetQuest: Enumerating all possible biosynthetic pathways in metabolic networks
8 versions - Latest release: about 4 years ago - 1 dependent package - 1 dependent repositories - 192 downloads last month - 2 maintainers
hankshaw 2.0.0
Model for The Evolution of Cooperation by the Hankshaw Effect
3 versions - Latest release: almost 10 years ago - 2 dependent repositories - 23 downloads last month - 1 stars on GitHub - 1 maintainer
alphafold3 0.0.8 💰
Paper - Pytorch
5 versions - Latest release: over 1 year ago - 156 downloads last month - 792 stars on GitHub - 1 maintainer
grpredict 25.6.1
Estimate growth curves using an Extended Kalman Filter
1 version - Latest release: 6 months ago - 236 downloads last month - 1 stars on GitHub - 1 maintainer
p3gpt 0.1.0
Precious3 GPT - A multimodal language model for biomedical applications
1 version - Latest release: 8 months ago - 6 downloads last month - 11 stars on GitHub - 1 maintainer
ypkpathway 3.0.1
Simulation and documentation of metabolic pathway assemblies using the Yeast Pathway Kit.
25 versions - Latest release: over 6 years ago - 2 dependent repositories - 68 downloads last month - 2 stars on GitHub - 1 maintainer
Top 8.0% on pypi.org
ndex2 3.11.0
Nice CX Python includes a client and a data model.
52 versions - Latest release: 4 months ago - 12 dependent packages - 33 dependent repositories - 48.2 thousand downloads last month - 6 stars on GitHub - 5 maintainers
optipyzer 0.4.1
Codon optimize DNA and Protein sequences for multiple species.
8 versions - Latest release: almost 3 years ago - 1 dependent repositories - 58 downloads last month - 27 stars on GitHub - 1 maintainer
plateo 0.3.1
Read/write microplate and picklist data for lab automation
8 versions - Latest release: 6 months ago - 1 dependent repositories - 203 downloads last month - 45 stars on GitHub - 1 maintainer
atlasapprox-disease 0.1.4
Cell atlas approximations for diseases, Python API
5 versions - Latest release: 9 months ago - 42 downloads last month - 0 stars on GitHub - 1 maintainer
dipwmsearch 0.1.8
Provides functions to search for any di-nucleotidic Position Weight Matrix (di-PWM) in a genomic ...
13 versions - Latest release: over 2 years ago - 1 dependent repositories - 52 downloads last month - 0 stars on gite.lirmm.fr - 2 maintainers
fis-calculator 0.0.1
FIS calculator for neurological protein-protein interactions
1 version - Latest release: over 2 years ago - 10 downloads last month - 1 maintainer
biosimulators-tellurium 0.1.44
BioSimulators-compliant command-line interface to the Tellurium/roadrunner simulator <https://tel...
40 versions - Latest release: about 1 year ago - 3 dependent repositories - 660 downloads last month - 2 stars on GitHub - 2 maintainers
pacbiodataprocessing 1.3.0
Tools to process PacBio sequencing data at molecule level
24 versions - Latest release: almost 3 years ago - 1 dependent repositories - 78 downloads last month - 0 stars on gitlab.com - 1 maintainer
phenopype-plugins 0.2.0
AI and other plugins for phenopype
5 versions - Latest release: 10 months ago - 24 downloads last month - 1 maintainer
snapgenefilereader 0.1.11
A Python project to read and write Snapgene *.dna into dict, json, and biopython object.
8 versions - Latest release: almost 8 years ago - 1 dependent repositories - 276 downloads last month - 1 maintainer
symbac 0.4.0
A package for generating synthetic images of bactera in phase contrast or fluorescence. Used for ...
13 versions - Latest release: over 1 year ago - 1 dependent repositories - 96 downloads last month - 18 stars on GitHub - 1 maintainer
megaqc 0.2.0
Collect and visualise data across multiple MultiQC runs
2 versions - Latest release: about 5 years ago - 1 dependent repositories - 36 downloads last month - 97 stars on GitHub - 1 maintainer
rafm 1.1.4
rafm
10 versions - Latest release: almost 4 years ago - 1 dependent repositories - 39 downloads last month - 2 stars on GitHub - 1 maintainer
hydra-genetics 3.3.0
Helper tools for use with hydra-genetics pipelines.
66 versions - Latest release: 10 days ago - 23 dependent repositories - 3.09 thousand downloads last month - 3 stars on GitHub - 1 maintainer
nafcodec 0.3.1
PyO3 bindings and Python interface to nafcodec, an encoder/decoder for Nucleotide Archive Format ...
4 versions - Latest release: 10 months ago - 381 downloads last month - 6 stars on GitHub - 1 maintainer
cana 1.0.0
This package implements a series of methods used to study control, canalization and redundancy in...
8 versions - Latest release: over 1 year ago - 130 downloads last month - 25 stars on GitHub - 3 maintainers
multiqc-msk 1.11.dev0
Create aggregate bioinformatics analysis reports across many samples and tools
1 version - Latest release: over 4 years ago - 1 dependent repositories - 13 downloads last month - 1,353 stars on GitHub - 1 maintainer
biosimulators-copasi 0.2.23
BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.
48 versions - Latest release: 12 months ago - 2 dependent repositories - 659 downloads last month - 2 stars on GitHub - 2 maintainers
lle7ch 1.0
Controls SOLA light engine.
3 versions - Latest release: about 7 years ago - 1 dependent repositories - 16 downloads last month - 2 stars on GitHub - 1 maintainer
hiconet 0.5.4
Hierachical Community Network, data driven omics integration
4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 25 downloads last month - 3 stars on GitHub - 1 maintainer
pymangal 0.3.0
A client library for the mangal API
1 version - Latest release: over 10 years ago - 2 dependent repositories - 7 downloads last month - 2 stars on GitHub - 1 maintainer
ogilo-array 0.0.3
Automated construction of oligo library sequences for oligo array synthesis.
3 versions - Latest release: 9 months ago - 11 downloads last month - 0 stars on GitHub - 1 maintainer
pygeno 2.0.0
A python package for Personalized Genomics and Proteomics
18 versions - Latest release: over 5 years ago - 1 dependent repositories - 183 downloads last month - 319 stars on GitHub - 2 maintainers
Top 3.3% on pypi.org
pydna 5.5.4
Representing double stranded DNA and functions for simulating cloning and homologous recombinatio...
119 versions - Latest release: 11 days ago - 7 dependent packages - 15 dependent repositories - 12 thousand downloads last month - 205 stars on GitHub - 2 maintainers