Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "bioinformatics" keyword
Top 0.3% on pypi.org
178 versions - Latest release: 14 days ago - 426 dependent packages - 11,467 dependent repositories - 2.86 million downloads last month - 20,598 stars on GitHub - 5 maintainers
dash 2.17.0 💰
A Python framework for building reactive web-apps. Developed by Plotly.178 versions - Latest release: 14 days ago - 426 dependent packages - 11,467 dependent repositories - 2.86 million downloads last month - 20,598 stars on GitHub - 5 maintainers
Top 0.6% on pypi.org
60 versions - Latest release: 4 months ago - 833 dependent packages - 3,405 dependent repositories - 815 thousand downloads last month - 3,908 stars on GitHub - 5 maintainers
biopython 1.83
Freely available tools for computational molecular biology.60 versions - Latest release: 4 months ago - 833 dependent packages - 3,405 dependent repositories - 815 thousand downloads last month - 3,908 stars on GitHub - 5 maintainers
Top 3.8% on pypi.org
26 versions - Latest release: about 1 month ago - 8 dependent packages - 5 dependent repositories - 234 thousand downloads last month - 163 stars on GitHub - 3 maintainers
bioframe 0.6.4
Operations and utilities for Genomic Interval Dataframes.26 versions - Latest release: about 1 month ago - 8 dependent packages - 5 dependent repositories - 234 thousand downloads last month - 163 stars on GitHub - 3 maintainers
Top 1.7% on pypi.org
83 versions - Latest release: about 1 month ago - 389 dependent packages - 467 dependent repositories - 192 thousand downloads last month - 501 stars on GitHub - 3 maintainers
anndata 0.10.7
Annotated data.83 versions - Latest release: about 1 month ago - 389 dependent packages - 467 dependent repositories - 192 thousand downloads last month - 501 stars on GitHub - 3 maintainers
Top 2.0% on pypi.org
18 versions - Latest release: over 2 years ago - 28 dependent packages - 61 dependent repositories - 149 thousand downloads last month - 484 stars on GitHub - 1 maintainer
edlib 1.3.9
Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.18 versions - Latest release: over 2 years ago - 28 dependent packages - 61 dependent repositories - 149 thousand downloads last month - 484 stars on GitHub - 1 maintainer
Top 1.2% on pypi.org
78 versions - Latest release: about 1 month ago - 416 dependent packages - 493 dependent repositories - 149 thousand downloads last month - 1,775 stars on GitHub - 3 maintainers
scanpy 1.10.1
Single-Cell Analysis in Python.78 versions - Latest release: about 1 month ago - 416 dependent packages - 493 dependent repositories - 149 thousand downloads last month - 1,775 stars on GitHub - 3 maintainers
Top 1.1% on pypi.org
10 versions - Latest release: 4 months ago - 20 dependent packages - 166 dependent repositories - 119 thousand downloads last month - 564 stars on GitHub - 4 maintainers
dash-cytoscape 1.0.0 💰
A Component Library for Dash aimed at facilitating network visualization in Python, wrapped aroun...10 versions - Latest release: 4 months ago - 20 dependent packages - 166 dependent repositories - 119 thousand downloads last month - 564 stars on GitHub - 4 maintainers
Top 1.9% on pypi.org
88 versions - Latest release: 4 months ago - 76 dependent packages - 268 dependent repositories - 111 thousand downloads last month - 440 stars on GitHub - 1 maintainer
pyfaidx 0.8.1
pyfaidx: efficient pythonic random access to fasta subsequences88 versions - Latest release: 4 months ago - 76 dependent packages - 268 dependent repositories - 111 thousand downloads last month - 440 stars on GitHub - 1 maintainer
Top 5.6% on pypi.org
59 versions - Latest release: 10 months ago - 6 dependent packages - 28 dependent repositories - 87.4 thousand downloads last month - 17 stars on GitHub - 2 maintainers
bioutils 0.5.8
miscellaneous simple bioinformatics utilities and lookup tables59 versions - Latest release: 10 months ago - 6 dependent packages - 28 dependent repositories - 87.4 thousand downloads last month - 17 stars on GitHub - 2 maintainers
Top 6.9% on pypi.org
85 versions - Latest release: 18 days ago - 2 dependent repositories - 67.2 thousand downloads last month - 6 maintainers
basepair 2.1.1
Python client for Basepair's API85 versions - Latest release: 18 days ago - 2 dependent repositories - 67.2 thousand downloads last month - 6 maintainers
Top 2.1% on pypi.org
20 versions - Latest release: about 2 years ago - 14 dependent packages - 51 dependent repositories - 65.5 thousand downloads last month - 683 stars on GitHub - 1 maintainer
biopandas 0.4.1
Machine Learning Library Extensions20 versions - Latest release: about 2 years ago - 14 dependent packages - 51 dependent repositories - 65.5 thousand downloads last month - 683 stars on GitHub - 1 maintainer
Top 4.6% on pypi.org
45 versions - Latest release: 3 months ago - 10 dependent packages - 21 dependent repositories - 63.8 thousand downloads last month - 38 stars on GitHub - 2 maintainers
biocommons.seqrepo 0.6.9
Non-redundant, compressed, journalled, file-based storage for biological sequences45 versions - Latest release: 3 months ago - 10 dependent packages - 21 dependent repositories - 63.8 thousand downloads last month - 38 stars on GitHub - 2 maintainers
Top 4.8% on pypi.org
122 versions - Latest release: 2 months ago - 3 dependent packages - 15 dependent repositories - 63.7 thousand downloads last month - 45 stars on GitHub - 1 maintainer
sevenbridges-python 2.11.0
SBG API python client bindings122 versions - Latest release: 2 months ago - 3 dependent packages - 15 dependent repositories - 63.7 thousand downloads last month - 45 stars on GitHub - 1 maintainer
Top 2.2% on pypi.org
93 versions - Latest release: 4 months ago - 43 dependent packages - 99 dependent repositories - 62.7 thousand downloads last month - 357 stars on GitHub - 1 maintainer
cyvcf2 0.30.28 💰
fast vcf parsing with cython + htslib93 versions - Latest release: 4 months ago - 43 dependent packages - 99 dependent repositories - 62.7 thousand downloads last month - 357 stars on GitHub - 1 maintainer
Top 3.5% on pypi.org
37 versions - Latest release: about 1 year ago - 21 dependent packages - 28 dependent repositories - 50 thousand downloads last month - 202 stars on GitHub - 2 maintainers
pybigwig 0.3.22
A package for accessing bigWig files using libBigWig37 versions - Latest release: about 1 year ago - 21 dependent packages - 28 dependent repositories - 50 thousand downloads last month - 202 stars on GitHub - 2 maintainers
Top 2.0% on pypi.org
22 versions - Latest release: about 8 years ago - 12 dependent packages - 129 dependent repositories - 47.9 thousand downloads last month - 392 stars on GitHub - 1 maintainer
pyvcf 0.6.8
Variant Call Format (VCF) parser for Python22 versions - Latest release: about 8 years ago - 12 dependent packages - 129 dependent repositories - 47.9 thousand downloads last month - 392 stars on GitHub - 1 maintainer
Top 2.4% on pypi.org
150 versions - Latest release: about 1 month ago - 10 dependent packages - 43 dependent repositories - 40.5 thousand downloads last month - 925 stars on GitHub - 2 maintainers
hail 0.2.130
Scalable library for exploring and analyzing genomic data.150 versions - Latest release: about 1 month ago - 10 dependent packages - 43 dependent repositories - 40.5 thousand downloads last month - 925 stars on GitHub - 2 maintainers
Top 7.8% on pypi.org
30 versions - Latest release: 4 months ago - 10 dependent packages - 47 dependent repositories - 38 thousand downloads last month - 7 stars on GitHub - 4 maintainers
yacman 0.9.3
A standardized configuration object for reference genome assemblies30 versions - Latest release: 4 months ago - 10 dependent packages - 47 dependent repositories - 38 thousand downloads last month - 7 stars on GitHub - 4 maintainers
Top 3.0% on pypi.org
73 versions - Latest release: over 1 year ago - 7 dependent packages - 34 dependent repositories - 37.5 thousand downloads last month - 231 stars on GitHub - 2 maintainers
hgvs 1.5.4
HGVS Parser, Formatter, Mapper, Validator73 versions - Latest release: over 1 year ago - 7 dependent packages - 34 dependent repositories - 37.5 thousand downloads last month - 231 stars on GitHub - 2 maintainers
Top 4.4% on pypi.org
5 versions - Latest release: 3 months ago - 13 dependent packages - 51 dependent repositories - 34 thousand downloads last month - 85 stars on GitHub - 1 maintainer
pyliftover 0.4.1
Pure-python implementation of UCSC ``liftOver`` genome coordinate conversion.5 versions - Latest release: 3 months ago - 13 dependent packages - 51 dependent repositories - 34 thousand downloads last month - 85 stars on GitHub - 1 maintainer
Top 2.2% on pypi.org
27 versions - Latest release: over 2 years ago - 2 dependent packages - 40 dependent repositories - 33 thousand downloads last month - 3 stars on GitHub - 4 maintainers
refgenconf 0.12.2
A standardized configuration object for reference genome assemblies27 versions - Latest release: over 2 years ago - 2 dependent packages - 40 dependent repositories - 33 thousand downloads last month - 3 stars on GitHub - 4 maintainers
Top 1.3% on pypi.org
66 versions - Latest release: over 8 years ago - 20 dependent packages - 88 dependent repositories - 29.6 thousand downloads last month - 487 stars on GitHub - 1 maintainer
cutadapt 1.9.1
Adapter trimming and other preprocessing of high-throughput sequencing reads66 versions - Latest release: over 8 years ago - 20 dependent packages - 88 dependent repositories - 29.6 thousand downloads last month - 487 stars on GitHub - 1 maintainer
Top 2.6% on pypi.org
13 versions - Latest release: about 1 month ago - 9 dependent packages - 29 dependent repositories - 28.6 thousand downloads last month - 9 stars on GitHub - 1 maintainer
prefixmaps 0.2.4
A python library for retrieving semantic prefix maps13 versions - Latest release: about 1 month ago - 9 dependent packages - 29 dependent repositories - 28.6 thousand downloads last month - 9 stars on GitHub - 1 maintainer
Top 9.0% on pypi.org
3 versions - Latest release: almost 5 years ago - 1 dependent package - 15 dependent repositories - 27.2 thousand downloads last month - 6 stars on GitHub - 1 maintainer
deeptoolsintervals 0.1.9
A python module creating/accessing GTF-based interval trees with associated meta-data3 versions - Latest release: almost 5 years ago - 1 dependent package - 15 dependent repositories - 27.2 thousand downloads last month - 6 stars on GitHub - 1 maintainer
Top 1.8% on pypi.org
15 versions - Latest release: 2 months ago - 17 dependent packages - 178 dependent repositories - 26.6 thousand downloads last month - 1,601 stars on GitHub - 3 maintainers
scispacy 0.5.4
A full SpaCy pipeline and models for scientific/biomedical documents.15 versions - Latest release: 2 months ago - 17 dependent packages - 178 dependent repositories - 26.6 thousand downloads last month - 1,601 stars on GitHub - 3 maintainers
Top 2.8% on pypi.org
78 versions - Latest release: 24 days ago - 19 dependent packages - 93 dependent repositories - 26.4 thousand downloads last month - 217 stars on GitHub - 1 maintainer
pronto 2.5.7
Python frontend to ontologies.78 versions - Latest release: 24 days ago - 19 dependent packages - 93 dependent repositories - 26.4 thousand downloads last month - 217 stars on GitHub - 1 maintainer
pipestat 0.9.1
A pipeline results reporter36 versions - Latest release: 23 days ago - 4 dependent packages - 3 dependent repositories - 25.9 thousand downloads last month - 4 stars on GitHub - 2 maintainers
Top 1.8% on pypi.org
24 versions - Latest release: 5 months ago - 15 dependent packages - 27 dependent repositories - 24.3 thousand downloads last month - 52 stars on GitHub - 2 maintainers
dnaio 1.2.0
Read and write FASTA and FASTQ files efficiently24 versions - Latest release: 5 months ago - 15 dependent packages - 27 dependent repositories - 24.3 thousand downloads last month - 52 stars on GitHub - 2 maintainers
Top 9.0% on pypi.org
120 versions - Latest release: 8 days ago - 1 dependent repositories - 22 thousand downloads last month - 3 stars on GitHub - 1 maintainer
gencove 2.16.3
Gencove API and CLI tool120 versions - Latest release: 8 days ago - 1 dependent repositories - 22 thousand downloads last month - 3 stars on GitHub - 1 maintainer
Top 5.9% on pypi.org
33 versions - Latest release: 22 days ago - 7 dependent packages - 4 dependent repositories - 22 thousand downloads last month - 67 stars on GitHub - 2 maintainers
bed-reader 1.0.4
Read and write the PLINK BED format, simply and efficiently.33 versions - Latest release: 22 days ago - 7 dependent packages - 4 dependent repositories - 22 thousand downloads last month - 67 stars on GitHub - 2 maintainers
Top 1.9% on pypi.org
36 versions - Latest release: 11 days ago - 23 dependent packages - 23 dependent repositories - 19.8 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-util 24.0.2
Galaxy generic utilities36 versions - Latest release: 11 days ago - 23 dependent packages - 23 dependent repositories - 19.8 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.0% on pypi.org
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
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
Top 1.6% on pypi.org
60 versions - Latest release: 11 days ago - 16 dependent packages - 43 dependent repositories - 19.6 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-tool-util 24.0.2
Galaxy tool and tool dependency utilities60 versions - Latest release: 11 days ago - 16 dependent packages - 43 dependent repositories - 19.6 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.2% on pypi.org
27 versions - Latest release: over 4 years ago - 6 dependent packages - 24 dependent repositories - 18.7 thousand downloads last month - 55 stars on GitHub - 2 maintainers
eutils 0.6.0
"Python interface to NCBI's eutilities API"27 versions - Latest release: over 4 years ago - 6 dependent packages - 24 dependent repositories - 18.7 thousand downloads last month - 55 stars on GitHub - 2 maintainers
Top 5.8% on pypi.org
25 versions - Latest release: 29 days ago - 1 dependent package - 11 dependent repositories - 18.6 thousand downloads last month - 45 stars on GitHub - 4 maintainers
piper 0.14.1
A lightweight python toolkit for gluing together restartable, robust command line pipelines25 versions - Latest release: 29 days ago - 1 dependent package - 11 dependent repositories - 18.6 thousand downloads last month - 45 stars on GitHub - 4 maintainers
Top 2.9% on pypi.org
17 versions - Latest release: over 1 year ago - 8 dependent packages - 29 dependent repositories - 18.4 thousand downloads last month - 685 stars on GitHub - 1 maintainer
dgllife 0.3.2
DGL-based package for Life Science17 versions - Latest release: over 1 year ago - 8 dependent packages - 29 dependent repositories - 18.4 thousand downloads last month - 685 stars on GitHub - 1 maintainer
Top 3.1% on pypi.org
146 versions - Latest release: about 2 years ago - 26 dependent packages - 196 dependent repositories - 18.1 thousand downloads last month - 135 stars on GitHub - 1 maintainer
loompy 3.0.7
Work with Loom files for single-cell RNA-seq data146 versions - Latest release: about 2 years ago - 26 dependent packages - 196 dependent repositories - 18.1 thousand downloads last month - 135 stars on GitHub - 1 maintainer
mmcif-pdbx 2.0.1
Python utilities for PDBx/mmCIF storage model7 versions - Latest release: about 3 years ago - 3 dependent packages - 3 dependent repositories - 17.4 thousand downloads last month - 6 stars on GitHub - 3 maintainers
Top 2.2% on pypi.org
53 versions - Latest release: about 2 months ago - 18 dependent packages - 22 dependent repositories - 17.3 thousand downloads last month - 557 stars on GitHub - 2 maintainers
biotite 0.40.0
A comprehensive library for computational molecular biology53 versions - Latest release: about 2 months ago - 18 dependent packages - 22 dependent repositories - 17.3 thousand downloads last month - 557 stars on GitHub - 2 maintainers
Top 3.3% on pypi.org
45 versions - Latest release: 4 days ago - 5 dependent packages - 12 dependent repositories - 17 thousand downloads last month - 930 stars on GitHub - 3 maintainers
pytdc 0.4.14
Therapeutics Data Commons45 versions - Latest release: 4 days ago - 5 dependent packages - 12 dependent repositories - 17 thousand downloads last month - 930 stars on GitHub - 3 maintainers
Top 5.2% on pypi.org
59 versions - Latest release: 22 days ago - 18 dependent packages - 6 dependent repositories - 17 thousand downloads last month - 110 stars on GitHub - 1 maintainer
pyhmmer 0.10.12
Cython bindings and Python interface to HMMER3.59 versions - Latest release: 22 days ago - 18 dependent packages - 6 dependent repositories - 17 thousand downloads last month - 110 stars on GitHub - 1 maintainer
Top 2.5% on pypi.org
48 versions - Latest release: 3 months ago - 44 dependent packages - 37 dependent repositories - 17 thousand downloads last month - 197 stars on GitHub - 1 maintainer
gemmi 0.6.5
library for structural biology48 versions - Latest release: 3 months ago - 44 dependent packages - 37 dependent repositories - 17 thousand downloads last month - 197 stars on GitHub - 1 maintainer
Top 3.6% on pypi.org
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
pyfastx 2.1.0
pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file67 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 4.0% on pypi.org
5 versions - Latest release: over 5 years ago - 6 dependent packages - 22 dependent repositories - 16 thousand downloads last month - 161 stars on GitHub - 1 maintainer
markov-clustering 0.0.6.dev0
Implementation of the Markov clustering (MCL) algorithm in python.5 versions - Latest release: over 5 years ago - 6 dependent packages - 22 dependent repositories - 16 thousand downloads last month - 161 stars on GitHub - 1 maintainer
Top 2.7% on pypi.org
120 versions - Latest release: 8 days ago - 56 dependent packages - 56 dependent repositories - 15.5 thousand downloads last month - 389 stars on GitHub - 2 maintainers
pyranges 0.1.1
GenomicRanges for Python.120 versions - Latest release: 8 days ago - 56 dependent packages - 56 dependent repositories - 15.5 thousand downloads last month - 389 stars on GitHub - 2 maintainers
Top 4.7% on pypi.org
58 versions - Latest release: 4 months ago - 9 dependent packages - 25 dependent repositories - 14.9 thousand downloads last month - 35 stars on GitHub - 4 maintainers
peppy 0.40.1
A python-based project metadata manager for portable encapsulated projects58 versions - Latest release: 4 months ago - 9 dependent packages - 25 dependent repositories - 14.9 thousand downloads last month - 35 stars on GitHub - 4 maintainers
Top 4.1% on pypi.org
8 versions - Latest release: 3 months ago - 1 dependent package - 14 dependent repositories - 14.3 thousand downloads last month - 176 stars on GitHub - 2 maintainers
pegasus-wms.api 5.0.7
Pegasus Workflow Management System Python API8 versions - Latest release: 3 months ago - 1 dependent package - 14 dependent repositories - 14.3 thousand downloads last month - 176 stars on GitHub - 2 maintainers
Top 5.4% on pypi.org
8 versions - Latest release: 3 months ago - 6 dependent repositories - 14.1 thousand downloads last month - 176 stars on GitHub - 2 maintainers
pegasus-wms.common 5.0.7
Pegasus Workflow Management System Python Commons8 versions - Latest release: 3 months ago - 6 dependent repositories - 14.1 thousand downloads last month - 176 stars on GitHub - 2 maintainers
Top 8.1% on pypi.org
19 versions - Latest release: 6 months ago - 3 dependent packages - 6 dependent repositories - 13.9 thousand downloads last month - 4 stars on GitHub - 3 maintainers
eido 0.2.2
A project metadata validator19 versions - Latest release: 6 months ago - 3 dependent packages - 6 dependent repositories - 13.9 thousand downloads last month - 4 stars on GitHub - 3 maintainers
Top 2.2% on pypi.org
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
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
Top 4.7% on pypi.org
42 versions - Latest release: 11 days ago - 15 dependent repositories - 11.3 thousand downloads last month - 257 stars on GitHub - 2 maintainers
dsub 0.4.11
A command-line tool that makes it easy to submit and run batch scripts in the cloud42 versions - Latest release: 11 days ago - 15 dependent repositories - 11.3 thousand downloads last month - 257 stars on GitHub - 2 maintainers
Top 4.7% on pypi.org
23 versions - Latest release: 24 days ago - 1 dependent package - 5 dependent repositories - 10.4 thousand downloads last month - 130 stars on GitHub - 1 maintainer
geoparse 2.0.4
Python library to access Gene Expression Omnibus Database (GEO)23 versions - Latest release: 24 days ago - 1 dependent package - 5 dependent repositories - 10.4 thousand downloads last month - 130 stars on GitHub - 1 maintainer
Top 4.1% on pypi.org
34 versions - Latest release: 10 days ago - 1 dependent package - 70 dependent repositories - 10.4 thousand downloads last month - 131 stars on GitHub - 1 maintainer
snakefmt 0.10.2
The uncompromising Snakemake code formatter34 versions - Latest release: 10 days ago - 1 dependent package - 70 dependent repositories - 10.4 thousand downloads last month - 131 stars on GitHub - 1 maintainer
Top 7.4% on pypi.org
21 versions - Latest release: 23 days ago - 7 dependent packages - 1 dependent repositories - 9.73 thousand downloads last month - 508 stars on GitHub - 2 maintainers
pydeseq2 0.4.9
A python implementation of DESeq2.21 versions - Latest release: 23 days ago - 7 dependent packages - 1 dependent repositories - 9.73 thousand downloads last month - 508 stars on GitHub - 2 maintainers
Top 4.1% on pypi.org
8 versions - Latest release: over 1 year ago - 20 dependent packages - 16 dependent repositories - 9.65 thousand downloads last month - 175 stars on GitHub - 1 maintainer
harmonypy 0.0.9
A data integration algorithm.8 versions - Latest release: over 1 year ago - 20 dependent packages - 16 dependent repositories - 9.65 thousand downloads last month - 175 stars on GitHub - 1 maintainer
Top 4.3% on pypi.org
48 versions - Latest release: 9 days ago - 1 dependent package - 4 dependent repositories - 9.42 thousand downloads last month - 218 stars on GitHub - 4 maintainers
nf-core 2.14.1
Helper tools for use with nf-core Nextflow pipelines.48 versions - Latest release: 9 days ago - 1 dependent package - 4 dependent repositories - 9.42 thousand downloads last month - 218 stars on GitHub - 4 maintainers
Top 2.0% on pypi.org
36 versions - Latest release: about 16 hours ago - 7 dependent packages - 74 dependent repositories - 9.13 thousand downloads last month - 1,162 stars on GitHub - 1 maintainer
multiqc 1.22.1
Create aggregate bioinformatics analysis reports across many samples and tools36 versions - Latest release: about 16 hours ago - 7 dependent packages - 74 dependent repositories - 9.13 thousand downloads last month - 1,162 stars on GitHub - 1 maintainer
Top 7.4% on pypi.org
62 versions - Latest release: 4 months ago - 13 dependent packages - 3 dependent repositories - 7.81 thousand downloads last month - 122 stars on GitHub - 1 maintainer
pyrodigal 3.3.0
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.62 versions - Latest release: 4 months ago - 13 dependent packages - 3 dependent repositories - 7.81 thousand downloads last month - 122 stars on GitHub - 1 maintainer
Top 6.7% on pypi.org
16 versions - Latest release: about 1 year ago - 3 dependent packages - 3 dependent repositories - 7.8 thousand downloads last month - 55 stars on GitHub - 1 maintainer
igv-notebook 0.5.2
Package for embedding the igv.js genome visualization in IPython notebooks16 versions - Latest release: about 1 year ago - 3 dependent packages - 3 dependent repositories - 7.8 thousand downloads last month - 55 stars on GitHub - 1 maintainer
Top 2.5% on pypi.org
10 versions - Latest release: over 4 years ago - 6 dependent packages - 37 dependent repositories - 7.79 thousand downloads last month - 1 maintainer
nimfa 1.4.0
A Python module for nonnegative matrix factorization10 versions - Latest release: over 4 years ago - 6 dependent packages - 37 dependent repositories - 7.79 thousand downloads last month - 1 maintainer
Top 2.5% on pypi.org
36 versions - Latest release: 7 months ago - 16 dependent packages - 54 dependent repositories - 7.75 thousand downloads last month - 144 stars on GitHub - 2 maintainers
tskit 0.5.6
The tree sequence toolkit.36 versions - Latest release: 7 months ago - 16 dependent packages - 54 dependent repositories - 7.75 thousand downloads last month - 144 stars on GitHub - 2 maintainers
Top 5.5% on pypi.org
689 versions - Latest release: about 1 month ago - 11 dependent repositories - 7.61 thousand downloads last month - 364 stars on GitHub - 1 maintainer
arvados-python-client 2.7.2
Arvados client library689 versions - Latest release: about 1 month ago - 11 dependent repositories - 7.61 thousand downloads last month - 364 stars on GitHub - 1 maintainer
Top 1.4% on pypi.org
25 versions - Latest release: about 2 months ago - 43 dependent packages - 166 dependent repositories - 7.58 thousand downloads last month - 842 stars on GitHub - 4 maintainers
scikit-bio 0.6.0
Data structures, algorithms and educational resources for bioinformatics.25 versions - Latest release: about 2 months ago - 43 dependent packages - 166 dependent repositories - 7.58 thousand downloads last month - 842 stars on GitHub - 4 maintainers
Top 8.3% on pypi.org
15 versions - Latest release: about 2 years ago - 3 dependent packages - 2 dependent repositories - 7.43 thousand downloads last month - 34 stars on GitHub - 1 maintainer
python-codon-tables 0.1.12
Codon Usage Tables for Python, from kazusa.or.jp15 versions - Latest release: about 2 years ago - 3 dependent packages - 2 dependent repositories - 7.43 thousand downloads last month - 34 stars on GitHub - 1 maintainer
Top 3.3% on pypi.org
112 versions - Latest release: over 1 year ago - 7 dependent packages - 15 dependent repositories - 7.41 thousand downloads last month - 155 stars on GitHub - 2 maintainers
pydna 5.2.0
Representing double stranded DNA and functions for simulating cloning and homologous recombinatio...112 versions - Latest release: over 1 year ago - 7 dependent packages - 15 dependent repositories - 7.41 thousand downloads last month - 155 stars on GitHub - 2 maintainers
Top 4.6% on pypi.org
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
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 4.0% on pypi.org
38 versions - Latest release: almost 2 years ago - 5 dependent packages - 14 dependent repositories - 6.98 thousand downloads last month - 358 stars on GitHub - 1 maintainer
pdb-tools 2.5.0
A swiss army knife for PDB files.38 versions - Latest release: almost 2 years ago - 5 dependent packages - 14 dependent repositories - 6.98 thousand downloads last month - 358 stars on GitHub - 1 maintainer
Top 1.7% on pypi.org
24 versions - Latest release: 11 months ago - 33 dependent packages - 109 dependent repositories - 6.9 thousand downloads last month - 3 maintainers
dendropy 4.6.1
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...24 versions - Latest release: 11 months ago - 33 dependent packages - 109 dependent repositories - 6.9 thousand downloads last month - 3 maintainers
Top 5.0% on pypi.org
18 versions - Latest release: 6 months ago - 1 dependent package - 5 dependent repositories - 6.61 thousand downloads last month - 481 stars on GitHub - 1 maintainer
redun 0.17.0
Yet another redundant workflow engine.18 versions - Latest release: 6 months ago - 1 dependent package - 5 dependent repositories - 6.61 thousand downloads last month - 481 stars on GitHub - 1 maintainer
Top 3.5% on pypi.org
25 versions - Latest release: over 2 years ago - 1 dependent package - 10 dependent repositories - 5.97 thousand downloads last month - 67 stars on GitHub - 4 maintainers
refgenie 0.12.1
Refgenie creates a standardized folder structure for reference genome files and indexes. You can ...25 versions - Latest release: over 2 years ago - 1 dependent package - 10 dependent repositories - 5.97 thousand downloads last month - 67 stars on GitHub - 4 maintainers
Top 2.6% on pypi.org
71 versions - Latest release: about 2 years ago - 7 dependent packages - 63 dependent repositories - 5.6 thousand downloads last month - 508 stars on GitHub - 4 maintainers
dash-bio 1.0.2 💰
Dash components for bioinformatics71 versions - Latest release: about 2 years ago - 7 dependent packages - 63 dependent repositories - 5.6 thousand downloads last month - 508 stars on GitHub - 4 maintainers
scoring-matrices 0.2.0
Dependency free, Cython-compatible scoring matrices to use with biological sequences.3 versions - Latest release: 12 days ago - 3 dependent packages - 5.6 thousand downloads last month - 2 stars on GitHub - 1 maintainer
Top 6.1% on pypi.org
11 versions - Latest release: 3 months ago - 11 dependent packages - 2 dependent repositories - 5.37 thousand downloads last month - 130 stars on GitHub - 1 maintainer
decoupler 1.6.0
Ensemble of methods to infer biological activities from omics data11 versions - Latest release: 3 months ago - 11 dependent packages - 2 dependent repositories - 5.37 thousand downloads last month - 130 stars on GitHub - 1 maintainer
Top 9.9% on pypi.org
13 versions - Latest release: 5 months ago - 8 dependent packages - 22 dependent repositories - 5.35 thousand downloads last month - 3 stars on GitHub - 1 maintainer
barcode 1.0.4
Design and test NGS barcodes.13 versions - Latest release: 5 months ago - 8 dependent packages - 22 dependent repositories - 5.35 thousand downloads last month - 3 stars on GitHub - 1 maintainer
Top 5.3% on pypi.org
51 versions - Latest release: 6 months ago - 7 dependent packages - 10 dependent repositories - 5.35 thousand downloads last month - 46 stars on GitHub - 7 maintainers
ga4gh.vrs 0.8.5
"GA4GH Variation Representation Specification (VRS) reference implementation (https://github.com/...51 versions - Latest release: 6 months ago - 7 dependent packages - 10 dependent repositories - 5.35 thousand downloads last month - 46 stars on GitHub - 7 maintainers
Top 7.1% on pypi.org
4 versions - Latest release: over 2 years ago - 5 dependent packages - 11 dependent repositories - 5.22 thousand downloads last month - 50 stars on GitHub - 1 maintainer
pyvcf3 1.0.3 💰
Variant Call Format (VCF) parser for Python4 versions - Latest release: over 2 years ago - 5 dependent packages - 11 dependent repositories - 5.22 thousand downloads last month - 50 stars on GitHub - 1 maintainer
Top 5.5% on pypi.org
64 versions - Latest release: 3 months ago - 1 dependent package - 4 dependent repositories - 5.1 thousand downloads last month - 4 stars on GitHub - 5 maintainers
resdk 21.1.0
Resolwe SDK for Python64 versions - Latest release: 3 months ago - 1 dependent package - 4 dependent repositories - 5.1 thousand downloads last month - 4 stars on GitHub - 5 maintainers
Top 2.8% on pypi.org
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freesasa 2.2.1
Calculate solvent accessible surface areas of proteins27 versions - Latest release: 6 months ago - 11 dependent packages - 22 dependent repositories - 5.02 thousand downloads last month - 1 maintainer
Top 2.1% on pypi.org
29 versions - Latest release: about 2 months ago - 27 dependent packages - 49 dependent repositories - 4.87 thousand downloads last month - 1,691 stars on GitHub - 1 maintainer
mappy 2.28
Minimap2 python binding29 versions - Latest release: about 2 months ago - 27 dependent packages - 49 dependent repositories - 4.87 thousand downloads last month - 1,691 stars on GitHub - 1 maintainer
Top 4.7% on pypi.org
27 versions - Latest release: 4 months ago - 14 dependent packages - 37 dependent repositories - 4.65 thousand downloads last month - 78 stars on GitHub - 1 maintainer
vcfpy 0.13.8
Python 3 VCF library with good support for both reading and writing27 versions - Latest release: 4 months ago - 14 dependent packages - 37 dependent repositories - 4.65 thousand downloads last month - 78 stars on GitHub - 1 maintainer
hpo3 1.2.0
A Python package to work with the HPO Ontology using a Rust backend for faster performance13 versions - Latest release: about 2 months ago - 1 dependent package - 4.44 thousand downloads last month - 5 stars on GitHub - 1 maintainer
cpg-workflows 1.24.4
CPG workflows for Hail Batch103 versions - Latest release: 1 day ago - 1 dependent repositories - 4.32 thousand downloads last month - 0 stars on GitHub - 2 maintainers
Top 1.9% on pypi.org
44 versions - Latest release: about 4 years ago - 3 dependent packages - 79 dependent repositories - 4.2 thousand downloads last month - 171 stars on GitHub - 3 maintainers
ruffus 2.8.4
Light-weight Python Computational Pipeline Management44 versions - Latest release: about 4 years ago - 3 dependent packages - 79 dependent repositories - 4.2 thousand downloads last month - 171 stars on GitHub - 3 maintainers
Top 7.6% on pypi.org
34 versions - Latest release: almost 8 years ago - 12 dependent repositories - 4.2 thousand downloads last month - 19 stars on GitHub - 1 maintainer
toolshed 0.4.6 💰
Tools for data34 versions - Latest release: almost 8 years ago - 12 dependent repositories - 4.2 thousand downloads last month - 19 stars on GitHub - 1 maintainer
Top 5.9% on pypi.org
196 versions - Latest release: 1 day ago - 1 dependent package - 21 dependent repositories - 4.18 thousand downloads last month - 117 stars on GitHub - 6 maintainers
ontobio 2.8.25
Library for working with OBO Library Ontologies and associations196 versions - Latest release: 1 day ago - 1 dependent package - 21 dependent repositories - 4.18 thousand downloads last month - 117 stars on GitHub - 6 maintainers
pyopal 0.6.0
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.16 versions - Latest release: 9 days ago - 1 dependent package - 1 dependent repositories - 4.16 thousand downloads last month - 7 stars on GitHub - 1 maintainer
cpg-utils 5.0.10
Library of convenience functions specific to the CPG102 versions - Latest release: 1 day ago - 3 dependent repositories - 4.07 thousand downloads last month - 0 stars on GitHub - 2 maintainers
Top 8.8% on pypi.org
47 versions - Latest release: 6 months ago - 2 dependent packages - 13 dependent repositories - 4.03 thousand downloads last month - 22 stars on GitHub - 4 maintainers
pysnptools 0.5.11
PySnpTools47 versions - Latest release: 6 months ago - 2 dependent packages - 13 dependent repositories - 4.03 thousand downloads last month - 22 stars on GitHub - 4 maintainers
Top 3.2% on pypi.org
80 versions - Latest release: 6 months ago - 21 dependent packages - 40 dependent repositories - 3.97 thousand downloads last month - 324 stars on GitHub - 1 maintainer
allensdk 2.16.2
core libraries for the allensdk.80 versions - Latest release: 6 months ago - 21 dependent packages - 40 dependent repositories - 3.97 thousand downloads last month - 324 stars on GitHub - 1 maintainer
Top 3.6% on pypi.org
20 versions - Latest release: 4 months ago - 1 dependent package - 9 dependent repositories - 3.96 thousand downloads last month - 4 maintainers
presto 0.7.2
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.20 versions - Latest release: 4 months ago - 1 dependent package - 9 dependent repositories - 3.96 thousand downloads last month - 4 maintainers
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5 versions - Latest release: 7 months ago - 6 dependent packages - 21 dependent repositories - 3.63 thousand downloads last month - 566 stars on GitHub - 1 maintainer
grakel 0.1.10
A scikit-learn compatible library for graph kernels5 versions - Latest release: 7 months ago - 6 dependent packages - 21 dependent repositories - 3.63 thousand downloads last month - 566 stars on GitHub - 1 maintainer
Top 2.1% on pypi.org
45 versions - Latest release: 8 months ago - 22 dependent packages - 64 dependent repositories - 3.6 thousand downloads last month - 189 stars on GitHub - 2 maintainers
cooler 0.9.3
Sparse binary format for genomic interaction matrices.45 versions - Latest release: 8 months ago - 22 dependent packages - 64 dependent repositories - 3.6 thousand downloads last month - 189 stars on GitHub - 2 maintainers
trailblazer 21.5.15
Trailblazer is a tool to manage and track state of analyses268 versions - Latest release: 3 days ago - 1 dependent package - 1 dependent repositories - 3.57 thousand downloads last month - 5 stars on GitHub - 5 maintainers
Top 7.0% on pypi.org
13 versions - Latest release: over 2 years ago - 2 dependent repositories - 3.51 thousand downloads last month - 918 stars on GitHub - 1 maintainer
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a Deep Learning Based Toolkit for Drug Discovery13 versions - Latest release: over 2 years ago - 2 dependent repositories - 3.51 thousand downloads last month - 918 stars on GitHub - 1 maintainer
orange3-bioinformatics 4.8.2 💰
Orange Bioinformatics add-on for Orange data mining software package.37 versions - Latest release: about 2 months ago - 1 dependent package - 1 dependent repositories - 3.38 thousand downloads last month - 19 stars on GitHub - 4 maintainers
Top 9.7% on pypi.org
344 versions - Latest release: 5 days ago - 3 dependent repositories - 3.23 thousand downloads last month - 17 stars on GitHub - 5 maintainers
resolwe-bio 56.0.0
Bioinformatics pipelines for the Resolwe platform344 versions - Latest release: 5 days ago - 3 dependent repositories - 3.23 thousand downloads last month - 17 stars on GitHub - 5 maintainers
Top 4.7% on pypi.org
32 versions - Latest release: about 1 month ago - 5 dependent packages - 5 dependent repositories - 3.16 thousand downloads last month - 299 stars on GitHub - 3 maintainers
cellrank 2.0.4
CellRank: dynamics from multi-view single-cell data32 versions - Latest release: about 1 month ago - 5 dependent packages - 5 dependent repositories - 3.16 thousand downloads last month - 299 stars on GitHub - 3 maintainers
Top 3.5% on pypi.org
71 versions - Latest release: about 1 month ago - 15 dependent packages - 21 dependent repositories - 3.15 thousand downloads last month - 431 stars on GitHub - 3 maintainers
sourmash 4.8.8
tools for comparing biological sequences with k-mer sketches71 versions - Latest release: about 1 month ago - 15 dependent packages - 21 dependent repositories - 3.15 thousand downloads last month - 431 stars on GitHub - 3 maintainers
Top 7.6% on pypi.org
281 versions - Latest release: 4 months ago - 1 dependent package - 4 dependent repositories - 3.11 thousand downloads last month - 68 stars on GitHub - 6 maintainers
tibanna 5.2.0
Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.281 versions - Latest release: 4 months ago - 1 dependent package - 4 dependent repositories - 3.11 thousand downloads last month - 68 stars on GitHub - 6 maintainers
Top 5.8% on pypi.org
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plantcv 4.2.1
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