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Biology Python Packages

Python packages with the GitHub topic biology. Sorted by relevance, with stars and monthly downloads.
deepchem
deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

141K 7K 2K
mims-harvard
pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

108K 1K 211
lmdu
pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

88K 294 24
Opentrons
opentrons

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

75K 500 199
Opentrons
opentrons-shared-data

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

54K 500 199
cogent3
cogent3

Comparative Genomics Toolkit 3

25K 134 67
laminlabs
pertdb

Registries for perturbations and their targets.

25K 4 1
pydna-group
pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

22K 224 48
histolab
histolab

Library for Digital Pathology Image Processing

13K 456 66
coredipper
operon-ai

Biologically Inspired Architectures for EpiAgentic Control

12K 29 2
openbraininstitute
bluecellulab

Biologically detailed neural network simulations and analysis API

11K 4 2
ylab-hi
deepchopper-cli

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

9K 8 1
gyorilab
indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

8K 209 77
omic
attest-py

A claim-native database for building reality models

8K 2 1
YaoYinYing
rosettapy

A Python utility for wrapping Rosetta command line tools.

8K 1 0
helicalAI
helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

7K 211 37
laminlabs
wetlab

Registries for perturbations and their targets.

7K 4 1
Ghini
ghini-desktop

plant collections manager (desktop version)

5K 26 14
pioreactor
pioreactor

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

5K 140 16
indralab
pybiopax

PyBioPAX: A python implementation of the BioPAX object model

5K 27 6
Imageomics
pybioclip

Python package and CLI that simplifies using the BioCLIP family of foundation models.

4K 61 13
ylab-hi
deepchopper

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

4K 8 1
omic
attestdb

A claim-native database for building reality models

4K 2 1
kblin
ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

3K 1K 178
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