Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

pypi.org "biology" keyword

sid 0.2.5
Image processing for seed images
6 versions - Latest release: over 4 years ago - 1 dependent repositories - 198 downloads last month - 1 stars on GitHub - 1 maintainer
gemeditor 0.4.0
A graphical editor for the reconstruction, annotation and testing of genome-scale models
21 versions - Latest release: over 6 years ago - 1 dependent repositories - 51 downloads last month - 1 stars on GitHub - 1 maintainer
betula 0.1.0
Optofluidic cell assay data analysis
1 version - Latest release: about 3 years ago - 1 dependent repositories - 22 downloads last month - 1 maintainer
idquant 1.0.1
Calculation of metabolite concentrations from C12 and C13 Mass Spectrometry Integrated Data
2 versions - Latest release: almost 3 years ago - 1 dependent repositories - 21 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: about 4 years ago - 1 dependent repositories - 127 downloads last month - 307 stars on GitHub - 2 maintainers
Top 4.3% on pypi.org
ncbi-genome-download 0.3.3
Download genome files from the NCBI FTP server.
25 versions - Latest release: 10 months ago - 3 dependent packages - 8 dependent repositories - 851 downloads last month - 886 stars on GitHub - 2 maintainers
deepchem-nightly 2.3.0
Deep learning models for drug discovery, quantum chemistry, and the life sciences.
33 versions - Latest release: almost 4 years ago - 1 dependent repositories - 114 downloads last month - 5,171 stars on GitHub - 1 maintainer
cenfind 0.14.0
Score cells for centrioles in IF data
32 versions - Latest release: 3 months ago - 159 downloads last month - 1 stars on GitHub - 1 maintainer
biosimulators-utils 0.1.187
Command-line program and library for reading, writing, validating and executing modeling projects...
179 versions - Latest release: 3 months ago - 4 dependent packages - 4 dependent repositories - 3.74 thousand downloads last month - 5 stars on GitHub - 2 maintainers
ndex-utils 3.0.11.8
NDEx Python utilities. Includes file conversion and importing functions
1 version - Latest release: 9 months ago - 1 dependent repositories - 1 maintainer
nicecx-dev 0.0.1b7
Nice CX Python includes a client and a data model.
14 versions - Latest release: over 6 years ago - 1 dependent repositories - 119 downloads last month - 1 maintainer
pydiopt 0.1.2
pyDIOPT - Python Wrapper for DIOPT
3 versions - Latest release: 10 days ago - 285 downloads last month - 0 stars on GitHub - 1 maintainer
bioprot 0.2.0
A package for DNA, RNA and protein sequence manipulation
1 version - Latest release: 10 days ago - 0 stars on GitHub
gemsembler 0.7.0
A tool for assembling and comparing several types of Genome-Scale Metabolic Models.
23 versions - Latest release: 10 days ago - 273 downloads last month - 3 maintainers
suchtree 1.1
A python library for doing fast, thread-safe computations on phylogenetic trees
8 versions - Latest release: 10 days ago - 1 dependent repositories - 268 downloads last month - 26 stars on GitHub - 1 maintainer
biosimulators-test-suite 0.1.88
Tools for validating that biosimulation tools are consistent with the BioSimulators standards
88 versions - Latest release: 10 months ago - 1 dependent repositories - 575 downloads last month - 7 stars on GitHub - 2 maintainers
Top 9.8% on pypi.org
tnseq-transit 3.3.4
TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface...
50 versions - Latest release: 3 months ago - 3 dependent repositories - 846 downloads last month - 16 stars on GitHub - 2 maintainers
Top 8.9% on pypi.org
snapatac2 2.6.3
SnapATAC2: Single-cell epigenomics analysis pipeline
25 versions - Latest release: 11 days ago - 2 dependent packages - 1 dependent repositories - 2.35 thousand downloads last month - 177 stars on GitHub - 1 maintainer
cocopye 0.4.0
Feature-based prediction of genome quality indices
11 versions - Latest release: 3 months ago - 93 downloads last month - 1 stars on GitHub - 1 maintainer
transit2 1.1.2
TRANSIT2 is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interfac...
18 versions - Latest release: 10 days ago - 405 downloads last month - 2 stars on GitHub - 1 maintainer
phenopype-plugins 0.1.2
Plugins for phenopype
3 versions - Latest release: 10 days ago - 69 downloads last month - 1 maintainer
sbsgenerator 1.0.5
Blazingly fast SBS matrix generator library
7 versions - Latest release: 2 months ago - 1.81 thousand downloads last month - 0 stars on GitHub - 1 maintainer
Top 6.3% on pypi.org
indra 1.22.0
Integrated Network and Dynamical Reasoning Assembler
28 versions - Latest release: over 1 year ago - 4 dependent packages - 10 dependent repositories - 794 downloads last month - 161 stars on GitHub - 1 maintainer
Top 8.0% on pypi.org
ndex2 3.8.0
Nice CX Python includes a client and a data model.
47 versions - Latest release: 4 months ago - 12 dependent packages - 33 dependent repositories - 17.7 thousand downloads last month - 6 stars on GitHub - 5 maintainers
biosimulators-copasi 0.1.35
BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.
35 versions - Latest release: about 2 years ago - 2 dependent repositories - 330 downloads last month - 2 stars on GitHub - 2 maintainers
methscan 1.0.0
command line tool for the analysis of single-cell bisulfite-sequencing data
1 version - Latest release: 2 months ago - 17 downloads last month - 2 stars on GitHub - 1 maintainer
moldrug 3.7.2
MolDrug (from Molecule to Drug) is a python package for drug-oriented optimization on the chemica...
34 versions - Latest release: 4 months ago - 1 dependent repositories - 275 downloads last month - 10 stars on GitHub - 1 maintainer
alphafold3 0.0.8 💰
Paper - Pytorch
5 versions - Latest release: 12 days ago - 636 downloads last month - 495 stars on GitHub - 1 maintainer
Top 8.8% on pypi.org
gauche 0.1.6
Gaussian Process Library for Molecules, Chemical Reactions and Proteins.
2 versions - Latest release: 6 months ago - 4 dependent repositories - 311 downloads last month - 179 stars on GitHub - 1 maintainer
chemical-converters 0.1.1
Chemical-Converters, developed by Knowledgator, showcases our technological capabilities in the c...
3 versions - Latest release: 3 months ago - 89 downloads last month - 1 maintainer
multiqc-sgr 1.21.4
Create aggregate bioinformatics analysis reports across many samples and tools
8 versions - Latest release: 12 days ago - 258 downloads last month - 0 stars on GitHub - 1 maintainer
Top 6.2% on pypi.org
itolapi 4.1.4
API for interacting with itol.embl.de
22 versions - Latest release: 4 months ago - 4 dependent packages - 12 dependent repositories - 1.14 thousand downloads last month - 31 stars on GitHub - 1 maintainer
bioontologies 0.4.3
Tools for biomedical ontologies.
20 versions - Latest release: 2 months ago - 4 dependent packages - 1 dependent repositories - 1.43 thousand downloads last month - 8 stars on GitHub - 1 maintainer
vivarium-core 1.6.4
Engine for composing and simulating computational biology models with the Vivarium interface.
135 versions - Latest release: 24 days ago - 1 dependent package - 13 dependent repositories - 463 downloads last month - 19 stars on GitHub - 3 maintainers
streq 0.0.2
Basic utilities for working with nucleotide sequence strings.
2 versions - Latest release: 12 months ago - 3 dependent packages - 1 dependent repositories - 18 downloads last month - 0 stars on GitHub - 1 maintainer
sc-supertree 2024.5.6
Spectral Cluster Supertree
3 versions - Latest release: 21 days ago - 1 dependent package - 101 downloads last month - 5 stars on GitHub - 1 maintainer
Top 8.1% on pypi.org
sbtab 1.0.8
SBtab - Standardised Data Tables for Systems Biology
89 versions - Latest release: 5 months ago - 4 dependent packages - 13 dependent repositories - 141 downloads last month - 1 maintainer
sbol-utilities-for-pudu 1.0a1
SBOL utilities
1 version - Latest release: 3 months ago - 1 dependent package - 29 downloads last month - 12 stars on GitHub - 1 maintainer
sbol3-for-pudu 1.0.0a1
Python implementation of SBOL 3 standard compatible with PUDU
1 version - Latest release: 8 months ago - 2 dependent packages - 7 downloads last month - 0 stars on GitHub - 1 maintainer
Top 8.4% on pypi.org
sbol2 1.4.1
Pure Python implementation of SBOL 2 standard
14 versions - Latest release: about 2 years ago - 2 dependent packages - 11 dependent repositories - 1.11 thousand downloads last month - 20 stars on GitHub - 2 maintainers
aleimi 0.0.2
Stochastic Conformation Analysis at semi empirical level with ab initio refinement for small mole...
5 versions - Latest release: 5 months ago - 67 downloads last month - 0 stars on GitHub - 1 maintainer
Top 3.6% on pypi.org
pyfastx 2.1.0
pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file
67 versions - Latest release: 3 months ago - 18 dependent packages - 28 dependent repositories - 16.7 thousand downloads last month - 235 stars on GitHub - 1 maintainer
Top 5.0% on pypi.org
pdb2pqr 3.6.2 💰
Automates many of the common tasks of preparing structures for continuum solvation calculations a...
16 versions - Latest release: 5 months ago - 3 dependent packages - 8 dependent repositories - 19.8 thousand downloads last month - 104 stars on GitHub - 3 maintainers
snipgenie 0.6.0 💰
variant calling and phylogenies from microbial WGS data
3 versions - Latest release: 5 months ago - 1 dependent repositories - 13 downloads last month - 8 stars on GitHub - 1 maintainer
Top 3.9% on pypi.org
mygene 3.2.2
Python Client for MyGene.Info services.
12 versions - Latest release: about 3 years ago - 33 dependent packages - 131 dependent repositories - 63.7 thousand downloads last month - 78 stars on GitHub - 2 maintainers
multiplierz 2.2.2
The MultiplierZ proteomics package
17 versions - Latest release: about 1 month ago - 2 dependent packages - 2 dependent repositories - 284 downloads last month - 21 stars on GitHub - 2 maintainers
ifpd2q 1.0.4
An iFISH probe design pipeline (II)
5 versions - Latest release: 3 months ago - 2 dependent packages - 72 downloads last month - 0 stars on GitHub - 1 maintainer
Top 7.2% on pypi.org
gilda 1.2.0
Grounding for biomedical entities with contextual disambiguation
19 versions - Latest release: 26 days ago - 8 dependent packages - 12 dependent repositories - 1.41 thousand downloads last month - 33 stars on GitHub - 1 maintainer
escher-legacy 1.7.4
Escher-legacy: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of...
1 version - Latest release: over 1 year ago - 1 dependent package - 52 downloads last month - 202 stars on GitHub - 1 maintainer
Top 4.6% on pypi.org
dnachisel 3.2.11
Optimize DNA sequences under constraints.
40 versions - Latest release: 12 months ago - 6 dependent packages - 6 dependent repositories - 7.26 thousand downloads last month - 205 stars on GitHub - 1 maintainer
Top 2.2% on pypi.org
cobra 0.29.0
COBRApy is a package for constraint-based modeling of metabolic networks.
99 versions - Latest release: 7 months ago - 56 dependent packages - 240 dependent repositories - 13.3 thousand downloads last month - 442 stars on GitHub - 5 maintainers
cellprofiler-library-nightly 5.0.0.dev65
cellprofiler-lirary implements CellProfiler's image processing and mathematical code, and is usab...
1 version - Latest release: 26 days ago - 2 dependent packages - 857 stars on GitHub - 1 maintainer
cellprofiler-core-nightly 5.0.0.dev65
cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
1 version - Latest release: 26 days ago - 1 dependent package - 857 stars on GitHub - 1 maintainer
ccapi 0.1.0
Python API for Cell Collective
1 version - Latest release: almost 2 years ago - 1 dependent package - 2 dependent repositories - 30 downloads last month - 12 stars on GitHub - 1 maintainer
Top 6.0% on pypi.org
cameo 0.13.6
cameo - computer aided metabolic engineering & optimization
46 versions - Latest release: over 2 years ago - 2 dependent packages - 31 dependent repositories - 645 downloads last month - 112 stars on GitHub - 1 maintainer
biosynonyms 0.0.1
A decentralized database of synonyms for biomedical concepts and entities.
1 version - Latest release: 4 months ago - 1 dependent package - 21 downloads last month - 0 stars on GitHub - 1 maintainer
beditor 2.0.1
A computational workflow for designing libraries of guide RNAs for CRISPR base editing
20 versions - Latest release: 4 months ago - 1 dependent repositories - 86 downloads last month - 14 stars on GitHub - 1 maintainer
treetop 2024.5.13.dev1
TreeTOP
1 version - Latest release: 14 days ago - 0 stars on GitHub - 1 maintainer
etfba 0.0.1
ETFBA is a package for constraints-based metabolic flux analysis
1 version - Latest release: 19 days ago - 130 downloads last month - 0 stars on GitHub - 1 maintainer
rust-sasa-python 0.1.0
An ultra-fast package for computing Solvent Accessible Surface Area (SASA/ASA) for proteins
1 version - Latest release: 29 days ago - 1.33 thousand downloads last month - 3 stars on GitHub - 1 maintainer
plasmidcanvas 1.0.0
A graphics package for creating customised plasmid maps
2 versions - Latest release: about 2 months ago - 256 downloads last month - 1 stars on GitHub - 2 maintainers
bioencoder 0.2.1
A metric learning toolkit
4 versions - Latest release: 26 days ago - 128 downloads last month - 5 stars on GitHub - 1 maintainer
orcapy 1.0.1
Tool for predicting the origin of replication on circular bacterial chromosomes
2 versions - Latest release: 3 months ago - 21 downloads last month - 11 stars on GitHub - 1 maintainer
protkit 0.3.0
A unified toolkit for structural protein engineering.
8 versions - Latest release: 18 days ago - 189 downloads last month - 28 stars on GitHub - 1 maintainer
cbsm 0.0.5
A compartment based scaledown model for modeling the dynamics of a bioreactor
6 versions - Latest release: 5 months ago - 46 downloads last month - 2 maintainers
phn 0.0.13
phn
13 versions - Latest release: 6 months ago - 97 downloads last month - 1 maintainer
ensc 0.0.4
ensc
4 versions - Latest release: 6 months ago - 2 dependent packages - 27 downloads last month - 1 maintainer
sbol-utilities 1.0a17
SBOL utilities
21 versions - Latest release: about 1 year ago - 1 dependent package - 1 dependent repositories - 93 downloads last month - 12 stars on GitHub - 2 maintainers
nafcodec 0.2.0
PyO3 bindings and Python interface to nafcodec, an encoder/decoder for Nucleotide Archive Format ...
2 versions - Latest release: about 2 months ago - 367 downloads last month - 3 stars on GitHub - 1 maintainer
pyuniprotkb 0.4.1
A python package to retrieve bioinformatics given Uniprot IDs.
7 versions - Latest release: about 1 month ago - 243 downloads last month - 3 stars on GitHub - 1 maintainer
yeastmlp 1.0.5
Python package for analysis of Multicellular-like phenotype formation in yeast species
9 versions - Latest release: 22 days ago - 119 downloads last month - 1 stars on GitHub - 1 maintainer
geom3d 0.0
Geometric Modeling on 3D Data
1 version - Latest release: 10 months ago - 29 downloads last month - 85 stars on GitHub - 1 maintainer
pynsm 1.0.1
A PyTorch implementation of non-negative similarity matching
2 versions - Latest release: 9 months ago - 23 downloads last month - 0 stars on GitHub - 1 maintainer
deepab-pytorch 0.0.1
Unofficial implementation of DeepAb in PyTorch.
1 version - Latest release: 11 months ago - 42 downloads last month - 1 stars on GitHub - 1 maintainer
biodatatypes 0.2.1
Nucleotide, amino acid, and codon datatypes for Python
2 versions - Latest release: 11 months ago - 27 downloads last month - 0 stars on GitHub - 1 maintainer
ogilo-array 0.0.2
Automated construction of oligo library sequences for oligo array synthesis.
2 versions - Latest release: 11 months ago - 16 downloads last month - 0 stars on GitHub - 1 maintainer
mach2 0.0.4
Migration Analysis of Clonal History 2
4 versions - Latest release: 7 months ago - 45 downloads last month - 2 stars on GitHub - 1 maintainer
genochain 0.0.7
Storing and versioning genomics data on a blockchain
2 versions - Latest release: about 1 year ago - 24 downloads last month - 1 maintainer
fis-calculator 0.0.1
FIS calculator for neurological protein-protein interactions
1 version - Latest release: about 1 year ago - 24 downloads last month - 1 maintainer
epitools 0.0.12
Quantifying 2D cell shape and epithelial tissue dynamics
12 versions - Latest release: 10 months ago - 162 downloads last month - 6 stars on GitHub - 1 maintainer
newick-tree-builder 0.4.17
Small lib to generate newick trees. Comes with NHX and rudimentary hybridization capabilities.
12 versions - Latest release: 12 months ago - 78 downloads last month - 0 stars on GitHub - 1 maintainer
conformine 0.0.1b14 removed
ConforMine, a predictor of conformational variability from amino acid sequence
4 versions - Latest release: about 1 year ago - 73 downloads last month - 1 maintainer
lib310-lite 0.1.1
lib310 Lite Python Package
52 versions - Latest release: 10 months ago - 292 downloads last month - 2 maintainers
tranception-pytorch-dohlee 0.0.5
Tranception - Pytorch
5 versions - Latest release: about 1 year ago - 41 downloads last month - 1 stars on GitHub - 1 maintainer
streamjsme 0.0.3
StreamJSME is a Streamlit component that use JSME to draw 2D molecules and use them on your Strea...
2 versions - Latest release: about 1 year ago - 34 downloads last month - 4 stars on GitHub - 1 maintainer
bpnet-pytorch 0.0.2
BPNet - Pytorch
1 version - Latest release: over 1 year ago - 29 downloads last month - 0 stars on GitHub - 1 maintainer
freeflux 0.3.6
FreeFlux is a package for 13C metabolic flux analysis
7 versions - Latest release: 3 months ago - 55 downloads last month - 8 stars on GitHub - 1 maintainer
lotkavolterra-simulator 1.0
Simulator of the Lotka-Volterra prey-predator system with demographic and observational noise and...
1 version - Latest release: over 1 year ago - 1 dependent package - 16 downloads last month - 2 stars on GitHub - 1 maintainer
coralme 1.0
Comprehensive Reconstruction Algorithm for ME-models (coralME)
1 version - Latest release: over 1 year ago - 10 downloads last month - 1 maintainer
super-beditor 1.2.0 removed
A computational workflow for designing libraries of guide RNAs for CRISPR base editing
2 versions - Latest release: over 1 year ago - 14 downloads last month - 1 maintainer
toff 0.1.0
toff is a python package to get topologies from the OpenFF initiative
5 versions - Latest release: 10 months ago - 42 downloads last month - 0 stars on GitHub - 1 maintainer
gene-fetchr 1.0.0b0
Search, retrieve, and scrape biological data from annotated genomes or public databases.
1 version - Latest release: over 1 year ago - 12 downloads last month - 1 maintainer
scip-workflows 0.1.2
3 versions - Latest release: about 1 year ago - 26 downloads last month - 1 maintainer
renku-bio 0.2.0
Renku plugin to annotate projects and datasets metadata with biological samples.
5 versions - Latest release: over 1 year ago - 36 downloads last month - 1 maintainer
med-signal 0.0.5
A biological signal simulation and evaluation package
3 versions - Latest release: over 1 year ago - 23 downloads last month - 0 stars on GitHub - 1 maintainer
pyncbi 0.1.6
Simple API for Python Integration with NCBI
9 versions - Latest release: almost 2 years ago - 1 dependent repositories - 21 downloads last month - 5 stars on GitHub - 1 maintainer
pacbiodataprocessing 1.3.0
Tools to process PacBio sequencing data at molecule level
24 versions - Latest release: over 1 year ago - 1 dependent repositories - 135 downloads last month - 0 stars on GitLab.com - 1 maintainer
woolf 0.1.1
A tool to built machine learning classifiers for protein function differentiation
1 version - Latest release: almost 5 years ago - 1 dependent repositories - 10 downloads last month - 1 stars on GitHub - 1 maintainer
wesci 0.6.2
We-Sci's seamless python toolset for tracking and managing research data
19 versions - Latest release: over 6 years ago - 1 dependent repositories - 152 downloads last month - 1 stars on GitHub - 1 maintainer
wc-sim 0.0.1
Sequential whole-cell model simulator
1 version - Latest release: 9 months ago - 1 dependent repositories - 6 stars on GitHub - 2 maintainers