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

orange-bioinformatics 2.6.25
Orange Bioinformatics add-on for Orange data mining software package.
59 versions - Latest release: over 6 years ago - 1 dependent repositories - 242 downloads last month - 7 maintainers
gff3tool 2.1.0
Python programs for processing GFF3 files
11 versions - Latest release: over 2 years ago - 1 dependent package - 1 dependent repositories - 121 downloads last month - 81 stars on GitHub - 7 maintainers
Top 5.3% on pypi.org
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 5.9% on pypi.org
ontobio 2.8.25
Library for working with OBO Library Ontologies and associations
196 versions - Latest release: 5 days ago - 1 dependent package - 21 dependent repositories - 4.18 thousand downloads last month - 117 stars on GitHub - 6 maintainers
Top 6.9% on pypi.org
basepair 2.1.1
Python client for Basepair's API
85 versions - Latest release: 21 days ago - 2 dependent repositories - 67.2 thousand downloads last month - 6 maintainers
Top 7.6% on pypi.org
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 5.5% on pypi.org
changeo 1.3.0
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
25 versions - Latest release: over 1 year ago - 1 dependent package - 7 dependent repositories - 689 downloads last month - 5 maintainers
Top 0.3% on pypi.org
dash 2.17.0 💰
A Python framework for building reactive web-apps. Developed by Plotly.
178 versions - Latest release: 18 days ago - 426 dependent packages - 11,467 dependent repositories - 2.86 million downloads last month - 20,598 stars on GitHub - 5 maintainers
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
chewbbaca 3.3.5
A complete suite for gene-by-gene schema creation and strain identification.
40 versions - Latest release: about 1 month ago - 1 dependent repositories - 398 downloads last month - 118 stars on GitHub - 5 maintainers
Top 9.0% on pypi.org
hicstuff 3.2.3
General purpose stuff to generate and handle Hi-C data in its simplest form.
130 versions - Latest release: 8 days ago - 1 dependent package - 4 dependent repositories - 1.89 thousand downloads last month - 35 stars on GitHub - 5 maintainers
extaxsi 0.3.9
Extaxsi is a bioinformatic library aimed to elaborate and visualize molecular and taxonomic infor...
11 versions - Latest release: over 2 years ago - 1 dependent repositories - 39 downloads last month - 4 stars on GitHub - 5 maintainers
Top 0.6% on pypi.org
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 5.5% on pypi.org
resdk 21.1.0
Resolwe SDK for Python
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
Top 5.5% on pypi.org
kipoiseq 0.7.1
kipoiseq: sequence-based data-loaders for Kipoi
21 versions - Latest release: over 2 years ago - 3 dependent packages - 62 dependent repositories - 1.9 thousand downloads last month - 76 stars on GitHub - 5 maintainers
trailblazer 21.5.15
Trailblazer is a tool to manage and track state of analyses
268 versions - Latest release: 6 days ago - 1 dependent package - 1 dependent repositories - 3.57 thousand downloads last month - 5 stars on GitHub - 5 maintainers
Top 9.7% on pypi.org
resolwe-bio 56.0.0
Bioinformatics pipelines for the Resolwe platform
344 versions - Latest release: 8 days ago - 3 dependent repositories - 3.23 thousand downloads last month - 17 stars on GitHub - 5 maintainers
kipoi-veff 0.3.1
kipoi_veff: variant effect prediction plugin for Kipoi
9 versions - Latest release: over 4 years ago - 1 dependent repositories - 160 downloads last month - 6 stars on GitHub - 4 maintainers
ngs-test-utils 0.0.5
Utilities for generation of synthetic NGS files
5 versions - Latest release: almost 4 years ago - 1 dependent repositories - 47 downloads last month - 0 stars on GitHub - 4 maintainers
Top 1.4% on pypi.org
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 1.1% on pypi.org
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 - 116 thousand downloads last month - 564 stars on GitHub - 4 maintainers
Top 5.8% on pypi.org
piper 0.14.1
A lightweight python toolkit for gluing together restartable, robust command line pipelines
25 versions - Latest release: about 1 month ago - 1 dependent package - 11 dependent repositories - 18.6 thousand downloads last month - 45 stars on GitHub - 4 maintainers
neuron-morphology 1.2.0
Tools for working with single-neuron morphological reconstructions
8 versions - Latest release: 22 days ago - 3 dependent packages - 1 dependent repositories - 87 downloads last month - 19 stars on GitHub - 4 maintainers
Top 6.9% on pypi.org
cogent 1.5.3
COmparative GENomics Toolkit
12 versions - Latest release: over 11 years ago - 24 dependent repositories - 197 downloads last month - 86 stars on GitHub - 4 maintainers
Top 3.5% on pypi.org
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
rose2 1.1.0
ROSE2 python package
4 versions - Latest release: over 4 years ago - 2 dependent repositories - 47 downloads last month - 11 stars on GitHub - 4 maintainers
Top 5.1% on pypi.org
kipoi 0.8.6
Kipoi: model zoo for genomics
73 versions - Latest release: almost 2 years ago - 2 dependent packages - 6 dependent repositories - 2.01 thousand downloads last month - 229 stars on GitHub - 4 maintainers
divvy 0.6.0
A python-based configuration manager for portable environment configurations
12 versions - Latest release: over 2 years ago - 1 dependent package - 5 dependent repositories - 302 downloads last month - 4 stars on GitHub - 4 maintainers
pararead 0.7.0
Parallel processing of sequencing reads
4 versions - Latest release: almost 5 years ago - 1 dependent package - 3 dependent repositories - 117 downloads last month - 8 stars on GitHub - 4 maintainers
kipoi-interpret 0.1.2
Kipoi interpret: interepretation plugin for Kipoi
3 versions - Latest release: about 5 years ago - 1 dependent repositories - 294 downloads last month - 3 stars on GitHub - 4 maintainers
Top 4.7% on pypi.org
peppy 0.40.1
A python-based project metadata manager for portable encapsulated projects
58 versions - Latest release: 4 months ago - 9 dependent packages - 25 dependent repositories - 16.2 thousand downloads last month - 35 stars on GitHub - 4 maintainers
Top 7.8% on pypi.org
yacman 0.9.3
A standardized configuration object for reference genome assemblies
30 versions - Latest release: 4 months ago - 10 dependent packages - 47 dependent repositories - 38 thousand downloads last month - 7 stars on GitHub - 4 maintainers
tobias 0.16.1
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
43 versions - Latest release: 5 months ago - 372 downloads last month - 172 stars on GitHub - 4 maintainers
Top 8.8% on pypi.org
pysnptools 0.5.11
PySnpTools
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
loopercli 0.12.6
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
8 versions - Latest release: about 4 years ago - 3 dependent repositories - 43 downloads last month - 19 stars on GitHub - 4 maintainers
Top 4.3% on pypi.org
nf-core 2.14.1
Helper tools for use with nf-core Nextflow pipelines.
48 versions - Latest release: 12 days ago - 1 dependent package - 4 dependent repositories - 8.96 thousand downloads last month - 217 stars on GitHub - 4 maintainers
biomaj-download 3.2.11
BioMAJ download service
41 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 488 downloads last month - 12 stars on GitHub - 4 maintainers
Top 2.2% on pypi.org
refgenconf 0.12.2
A standardized configuration object for reference genome assemblies
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
ngstk 0.0.1rc2
Next-generation sequencing utility functions
3 versions - Latest release: about 5 years ago - 1 dependent repositories - 29 downloads last month - 1 stars on GitHub - 4 maintainers
mixs-linkml 0.1.3
A LinkML model for the MIxS standard
3 versions - Latest release: about 2 years ago - 1 dependent repositories - 29 downloads last month - 33 stars on GitHub - 4 maintainers
Top 8.2% on pypi.org
fastlmm 0.6.8
Fast GWAS
52 versions - Latest release: 21 days ago - 1 dependent package - 7 dependent repositories - 680 downloads last month - 43 stars on GitHub - 4 maintainers
orange3-bioinformatics 4.8.2 💰
Orange Bioinformatics add-on for Orange data mining software package.
37 versions - Latest release: 2 months ago - 1 dependent package - 1 dependent repositories - 3.38 thousand downloads last month - 19 stars on GitHub - 4 maintainers
gwas_benchmark 0.1.3
GWAS benchmark
4 versions - Latest release: over 8 years ago - 26 downloads last month - 4 maintainers
hic2cool 1.0.1
Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (f...
28 versions - Latest release: 6 months ago - 1 dependent package - 1 dependent repositories - 1.19 thousand downloads last month - 53 stars on GitHub - 4 maintainers
Top 3.6% on pypi.org
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
Top 2.6% on pypi.org
dash-bio 1.0.2 💰
Dash components for bioinformatics
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
psicalc 0.6.1
Algorithm for clustering protein multiple sequence alignments using normalized mutual information.
49 versions - Latest release: about 1 month ago - 1 dependent repositories - 355 downloads last month - 2 stars on GitHub - 3 maintainers
fgpyo 0.3.0 💰
Python bioinformatics and genomics library
14 versions - Latest release: about 1 month ago - 1 dependent package - 1 dependent repositories - 877 downloads last month - 23 stars on GitHub - 3 maintainers
checkqc 4.0.2
A simple program to parse Illumina NGS data and check it for quality criteria.
37 versions - Latest release: 29 days ago - 1 dependent repositories - 504 downloads last month - 24 stars on GitHub - 3 maintainers
gen3-tracker 0.0.2
Commons utilities
24 versions - Latest release: about 2 months ago - 1 dependent package - 792 downloads last month - 1 stars on GitHub - 3 maintainers
galaxy-model-tools 19.9.0.dev2
Galaxy Model Tools`
1 version - Latest release: over 2 years ago - 1 dependent repositories - 9 downloads last month - 1,315 stars on GitHub - 3 maintainers
aviary-genome 0.9.1
aviary - metagenomics pipeline using long and short reads
21 versions - Latest release: 8 days ago - 193 downloads last month - 68 stars on GitHub - 3 maintainers
Top 8.1% on pypi.org
svtools 0.5.1
Tools for processing and analyzing structural variants
9 versions - Latest release: over 4 years ago - 3 dependent repositories - 242 downloads last month - 141 stars on GitHub - 3 maintainers
Top 3.3% on pypi.org
pytdc 0.4.14
Therapeutics Data Commons
47 versions - Latest release: 7 days ago - 5 dependent packages - 12 dependent repositories - 18.6 thousand downloads last month - 930 stars on GitHub - 3 maintainers
Top 7.2% on pypi.org
scikit-mdr 0.4.5
Multifactor Dimensionality Reduction (MDR)
11 versions - Latest release: 11 months ago - 3 dependent packages - 11 dependent repositories - 368 downloads last month - 126 stars on GitHub - 3 maintainers
bedshift 1.1.1
BED file perturbations
4 versions - Latest release: about 3 years ago - 1 dependent repositories - 31 downloads last month - 3 maintainers
ccmetagen 1.5.0
Microbiome classification pipeline
10 versions - Latest release: about 1 month ago - 1 dependent repositories - 170 downloads last month - 58 stars on GitHub - 3 maintainers
mmcif-pdbx 2.0.1
Python utilities for PDBx/mmCIF storage model
7 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 5.7% on pypi.org
google-nucleus 0.6.0
A library for reading and writing genomics data.
19 versions - Latest release: over 2 years ago - 1 dependent package - 34 dependent repositories - 238 downloads last month - 776 stars on GitHub - 3 maintainers
Top 1.7% on pypi.org
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
oxbow 0.3.1
Read specialized bioinformatic file formats into dataframes.
4 versions - Latest release: 4 months ago - 1 dependent package - 1 dependent repositories - 541 downloads last month - 44 stars on GitHub - 3 maintainers
Top 9.8% on pypi.org
hicexplorer 2.2.1
Set of programs to process, analyze and visualize Hi-C data
10 versions - Latest release: over 5 years ago - 3 dependent packages - 2 dependent repositories - 217 downloads last month - 216 stars on GitHub - 3 maintainers
thera-py 0.4.0
VICC normalization routine for therapies
34 versions - Latest release: over 1 year ago - 1 dependent package - 2 dependent repositories - 1.14 thousand downloads last month - 10 stars on GitHub - 3 maintainers
Top 5.1% on pypi.org
galaxy-web-stack 24.0.2
Galaxy web stack abstraction
18 versions - Latest release: 14 days ago - 5 dependent packages - 10 dependent repositories - 437 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 3.1% on pypi.org
airr 1.5.0
AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data.
7 versions - Latest release: 9 months ago - 7 dependent packages - 11 dependent repositories - 2.66 thousand downloads last month - 34 stars on GitHub - 3 maintainers
mitywgs 1.0.0 💰
A sensitive Mitochondrial variant detection pipeline from WGS data
10 versions - Latest release: 4 months ago - 1 dependent repositories - 107 downloads last month - 34 stars on GitHub - 3 maintainers
dgenies 1.5.0
Dotplot large Genomes in an Interactive, Efficient and Simple way
10 versions - Latest release: about 1 year ago - 1 dependent repositories - 133 downloads last month - 93 stars on GitHub - 3 maintainers
mwtab 1.2.5
Parser for mwtab files from the Metabolomics Workbench
20 versions - Latest release: about 2 years ago - 1 dependent package - 3 dependent repositories - 150 downloads last month - 11 stars on GitHub - 3 maintainers
caravel 0.13.2
Caravel provides aweb interface to interact with your PEP-formatted projects. Caravel lets you s...
3 versions - Latest release: over 4 years ago - 2 dependent repositories - 28 downloads last month - 3 maintainers
g3t-etl 0.0.1rc11
Commons utilities
11 versions - Latest release: about 2 months ago - 84 downloads last month - 1 stars on GitHub - 3 maintainers
Top 1.6% on pypi.org
galaxy-tool-util 24.0.2
Galaxy tool and tool dependency utilities
60 versions - Latest release: 14 days ago - 16 dependent packages - 43 dependent repositories - 19.6 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
mutagene 0.9.0
Mutational analysis with Python
29 versions - Latest release: about 4 years ago - 1 dependent repositories - 161 downloads last month - 3 maintainers
Top 5.3% on pypi.org
cooltools 0.7.0
Analysis tools for genomic interaction data stored in .cool format
14 versions - Latest release: 29 days ago - 3 dependent packages - 7 dependent repositories - 520 downloads last month - 120 stars on GitHub - 3 maintainers
bulker 0.7.3
Manager of portable multi-container computing environments
17 versions - Latest release: over 2 years ago - 1 dependent repositories - 203 downloads last month - 3 maintainers
Top 6.1% on pypi.org
galaxy-config 24.0.2
Galaxy configuration
16 versions - Latest release: 14 days ago - 3 dependent packages - 3 dependent repositories - 393 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 9.0% on pypi.org
pegasus-wms 5.0.7
Pegasus Workflow Management System Python Codebase
8 versions - Latest release: 3 months ago - 1 dependent package - 11 dependent repositories - 60 downloads last month - 176 stars on GitHub - 3 maintainers
aced-submission 0.0.7
Populate ACED commons from FHIR resources
26 versions - Latest release: 8 months ago - 201 downloads last month - 3 maintainers
Top 3.1% on pypi.org
galaxy-containers 22.1.1
Galaxy Container Modeling and Interaction Abstractions
6 versions - Latest release: over 1 year ago - 4 dependent packages - 13 dependent repositories - 2.96 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.2% on pypi.org
galaxy-auth 24.0.2
Galaxy auth framework and implementations
19 versions - Latest release: 14 days ago - 2 dependent packages - 10 dependent repositories - 396 downloads last month - 1,315 stars on GitHub - 3 maintainers
disease-normalizer 0.3.1
VICC normalization routine for diseases
26 versions - Latest release: over 1 year ago - 2 dependent packages - 3 dependent repositories - 2.43 thousand downloads last month - 4 stars on GitHub - 3 maintainers
Top 7.8% on pypi.org
svtyper 0.7.1
Bayesian genotyper for structural variants
4 versions - Latest release: over 4 years ago - 3 dependent repositories - 276 downloads last month - 116 stars on GitHub - 3 maintainers
galaxy-test-api 24.0.2
Galaxy API tests
18 versions - Latest release: 14 days ago - 1 dependent repositories - 186 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.7% on pypi.org
cellrank 2.0.4
CellRank: dynamics from multi-view single-cell data
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
Top 5.1% on pypi.org
galaxy-web-framework 24.0.2
Galaxy web framework
19 versions - Latest release: 14 days ago - 4 dependent packages - 10 dependent repositories - 423 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-selenium 24.0.2
Galaxy Selenium interaction framework
19 versions - Latest release: 14 days ago - 1 dependent repositories - 222 downloads last month - 1,315 stars on GitHub - 3 maintainers
rnanorm 2.1.0
Common RNA-seq normalization methods
14 versions - Latest release: 7 months ago - 1 dependent repositories - 1.11 thousand downloads last month - 52 stars on GitHub - 3 maintainers
il5pred 1.6
A tool to predict il5 inducing peptides
6 versions - Latest release: 9 months ago - 26 downloads last month - 2 stars on GitHub - 3 maintainers
uta-tools 0.1.3
Service for querying the biocommons.uta database
20 versions - Latest release: over 1 year ago - 2 dependent packages - 4 dependent repositories - 6 downloads last month - 4 stars on GitHub - 3 maintainers
sigpross 0.0.0.27
Decomposes mutational catalogues to mutational signatures
27 versions - Latest release: almost 4 years ago - 1 dependent repositories - 293 downloads last month - 146 stars on GitHub - 3 maintainers
Top 4.1% on pypi.org
galaxy-job-execution 24.0.2
Galaxy job execution runtime utilities
20 versions - Latest release: 14 days ago - 5 dependent packages - 10 dependent repositories - 430 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-web-apps 24.0.2
Galaxy web apps
15 versions - Latest release: 14 days ago - 2 dependent packages - 1 dependent repositories - 233 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 3.8% on pypi.org
galaxy-job-metrics 24.0.2
Galaxy job metrics
22 versions - Latest release: 14 days ago - 3 dependent packages - 10 dependent repositories - 665 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 3.4% on pypi.org
deeptools 3.5.5
Useful tools for exploring deep sequencing data.
60 versions - Latest release: 2 months ago - 6 dependent packages - 36 dependent repositories - 2.33 thousand downloads last month - 645 stars on GitHub - 3 maintainers
Top 5.4% on pypi.org
galaxy-files 24.0.2
Galaxy file source framework and default plugins
16 versions - Latest release: 14 days ago - 4 dependent packages - 6 dependent repositories - 499 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 7.4% on pypi.org
gtdbtk 2.4.0
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
48 versions - Latest release: 28 days ago - 2 dependent repositories - 403 downloads last month - 430 stars on GitHub - 3 maintainers
gene-normalizer 0.2.10
VICC normalization routine for genes
51 versions - Latest release: 10 months ago - 4 dependent packages - 6 dependent repositories - 2.72 thousand downloads last month - 1 stars on GitHub - 3 maintainers
Top 6.1% on pypi.org
galaxy-test-base 24.0.2
Galaxy testing utilities
18 versions - Latest release: 14 days ago - 2 dependent packages - 9 dependent repositories - 272 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.7% on pypi.org
sniffles 2.3.3
A fast structural variation caller for long-read sequencing data
12 versions - Latest release: 15 days ago - 1 dependent package - 3 dependent repositories - 769 downloads last month - 511 stars on GitHub - 3 maintainers
ga4gh.vrsatile.pydantic 0.2.0
"Translation of the GA4GH VRS and VRSATILE Schemas to a Pydantic data model"
24 versions - Latest release: 8 months ago - 7 dependent packages - 10 dependent repositories - 189 downloads last month - 0 stars on GitHub - 3 maintainers
Top 4.9% on pypi.org
galaxy-data 24.0.2
Galaxy datatype framework and datatypes
24 versions - Latest release: 14 days ago - 9 dependent packages - 13 dependent repositories - 782 downloads last month - 1,315 stars on GitHub - 3 maintainers