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

seqr-loader 1.2.5
The hail scripts in this repo can be used to pre-process variant callsets and export them to elas...
18 versions - Latest release: about 2 years ago - 1 dependent repositories - 109 downloads last month - 0 stars on GitHub - 2 maintainers
wgse-ng 0.0.2a0
Whole Genome Sequencing data manipulation tool
1 version - Latest release: 1 day ago - 2 stars on GitHub - 2 maintainers
boink 0.0.0
boink: streaming de Bruijn graph compaction and sketching.
2 versions - Latest release: over 4 years ago - 1 dependent repositories - 13 downloads last month - 8 stars on GitHub - 2 maintainers
mssw 0.1.5
Modern Cpp binding for complete-striped-smith-watern-library
5 versions - Latest release: over 1 year ago - 45 downloads last month - 3 stars on GitHub - 2 maintainers
dispbind 1.0.2
Disorder protein genomic binding analysis toolkit
2 versions - Latest release: over 1 year ago - 15 downloads last month - 2 stars on GitHub - 1 maintainer
sv2 1.4.3
SV2: Support Vector Structural Variation Genotyper
10 versions - Latest release: about 6 years ago - 1 dependent repositories - 202 downloads last month - 57 stars on GitHub - 2 maintainers
Top 4.0% on pypi.org
pdb-tools 2.5.0
A swiss army knife for PDB files.
38 versions - Latest release: almost 2 years ago - 2 dependent packages - 14 dependent repositories - 7.11 thousand downloads last month - 346 stars on GitHub - 1 maintainer
geneflow3 3.0.0a1
A light-weight, extendable workflow engine for scientific computing.
1 version - Latest release: over 2 years ago - 1 dependent repositories - 17 downloads last month - 0 stars on GitHub - 2 maintainers
Top 8.9% on pypi.org
seqlogo 5.29.9
Python port of the R Bioconductor `seqlogo` package
38 versions - Latest release: about 2 hours ago - 2 dependent packages - 3 dependent repositories - 495 downloads last month - 25 stars on GitHub - 2 maintainers
trailblazer 21.5.6
Trailblazer is a tool to manage and track state of analyses
259 versions - Latest release: about 3 hours ago - 1 dependent package - 1 dependent repositories - 2.08 thousand downloads last month - 5 stars on GitHub - 6 maintainers
scoring-matrices 0.1.0
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
1 version - Latest release: about 3 hours ago - 0 stars on GitHub - 1 maintainer
gccov 1.0.3
Visualize gc & coverage.
5 versions - Latest release: over 3 years ago - 1 dependent repositories - 34 downloads last month - 0 stars on GitHub - 2 maintainers
bioscripts.convert 0.4
Biopython scripts for converting molecular sequences between formats.
2 versions - Latest release: over 12 years ago - 2 dependent repositories - 16 downloads last month - 2 maintainers
Top 9.7% on pypi.org
resolwe-bio 55.4.0
Bioinformatics pipelines for the Resolwe platform
342 versions - Latest release: 18 days ago - 3 dependent repositories - 2.6 thousand downloads last month - 17 stars on GitHub - 5 maintainers
isoenum 0.4.1
InChI generator.
12 versions - Latest release: over 4 years ago - 1 dependent repositories - 22 downloads last month - 3 stars on GitHub - 4 maintainers
moldf 0.7.5
Super lightweight and fast mmCIF/PDB/MOL2 file parser into Pandas DataFrames and backwards writer.
6 versions - Latest release: 7 months ago - 83 downloads last month - 7 stars on GitHub - 2 maintainers
setriq 1.6.4
Python package written in C++ for pairwise distance computation for sequences.
11 versions - Latest release: over 1 year ago - 1 dependent repositories - 291 downloads last month - 15 stars on GitHub - 2 maintainers
bfscan 0.0.4
bfscan is designed to detect foodborne pathogens using bloom filter and machine learning
4 versions - Latest release: about 1 year ago - 18 downloads last month - 1 maintainer
structuremap 0.0.9
An open-source Python package of the AlphaPept ecosystem
9 versions - Latest release: about 1 year ago - 1 dependent repositories - 169 downloads last month - 25 stars on GitHub - 2 maintainers
cromshell-draft-release 2.0.0
Command Line Interface (CLI) for Cromwell servers
1 version - Latest release: about 1 year ago - 22 downloads last month - 53 stars on GitHub - 2 maintainers
pipestat 0.9.1
A pipeline results reporter
36 versions - Latest release: 9 days ago - 3 dependent packages - 3 dependent repositories - 18.1 thousand downloads last month - 4 stars on GitHub - 2 maintainers
ngstk 0.0.1rc2
Next-generation sequencing utility functions
3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 29 downloads last month - 1 stars on GitHub - 4 maintainers
hmmerclust 0.0.1.dev5
Detection and analysis of gene clusters in bacterial genomes.
5 versions - Latest release: almost 9 years ago - 3 dependent repositories - 57 downloads last month - 0 stars on GitHub - 2 maintainers
pyranges1 0.1.1
GenomicRanges for Python.
2 versions - Latest release: 2 days ago - 251 downloads last month - 2 stars on GitHub - 2 maintainers
Top 9.0% on pypi.org
gencove 2.16.2
Gencove API and CLI tool
119 versions - Latest release: 9 days ago - 1 dependent repositories - 6.77 thousand downloads last month - 3 stars on GitHub - 1 maintainer
pypop-genomics 1.0.2
PyPop: Python for Population Genomics
20 versions - Latest release: 2 months ago - 2.38 thousand downloads last month - 19 stars on GitHub - 1 maintainer
contextualized-ml 0.2.7
A statistical machine learning toolbox for estimating models, distributions, and functions with s...
9 versions - Latest release: 4 months ago - 103 downloads last month - 59 stars on GitHub - 1 maintainer
yasim 3.2.0
Yet Another SIMulator for Alternative Splicing Events and Realistic Gene Expression Profile
2 versions - Latest release: 4 months ago - 1 dependent package - 37 downloads last month - 0 stars on GitHub - 1 maintainer
autopvs1-batch 2.0
A tool for batch run autoPVS1
1 version - Latest release: over 2 years ago - 1 dependent repositories - 14 downloads last month - 28 stars on GitHub - 2 maintainers
wags-tails 0.1.3
Data acquisition tools for Wagnerds
4 versions - Latest release: about 1 month ago - 2 dependent packages - 1.93 thousand downloads last month - 0 stars on GitHub - 2 maintainers
biotdg 0.1.0
Bioinformatics Test Data Generator
1 version - Latest release: over 4 years ago - 1 dependent repositories - 23 downloads last month - 1 stars on GitHub - 4 maintainers
cromtool 1.4
Development tool for Cromwell
5 versions - Latest release: about 8 years ago - 2 dependent repositories - 26 downloads last month - 960 stars on GitHub - 1 maintainer
cxio 0.3.0
Utility to parse CX JSON streams
3 versions - Latest release: over 8 years ago - 2 dependent repositories - 14 downloads last month - 1 stars on GitHub - 2 maintainers
Top 4.7% on pypi.org
vcfpy 0.13.8
Python 3 VCF library with good support for both reading and writing
27 versions - Latest release: 4 months ago - 10 dependent packages - 37 dependent repositories - 4.65 thousand downloads last month - 78 stars on GitHub - 1 maintainer
pyopal 0.5.2
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
15 versions - Latest release: 2 months ago - 1 dependent repositories - 2.48 thousand downloads last month - 7 stars on GitHub - 2 maintainers
cirrocumulus 1.1.57
Bring your single-cell data to life
143 versions - Latest release: 7 months ago - 1 dependent repositories - 1.36 thousand downloads last month - 64 stars on GitHub - 3 maintainers
plinkliftover 0.5.2
Converts genotype data stored in plink's PED+MAP format from one genome build to another, using l...
7 versions - Latest release: 8 months ago - 1 dependent repositories - 64 downloads last month - 4 stars on GitHub - 2 maintainers
bambu-qsar 0.0.18
bambu (bioassays model builder) is CLI tool to build QSAR models based on PubChem BioAssays datasets
13 versions - Latest release: 11 months ago - 1 dependent repositories - 67 downloads last month - 3 stars on GitHub - 2 maintainers
grabseqs 0.7.0
Easily download reads from next-gen sequencing repositories like NCBI SRA
11 versions - Latest release: over 4 years ago - 1 dependent repositories - 86 downloads last month - 101 stars on GitHub - 1 maintainer
nanorepeat 1.4.1
NanoRepeat: quantification of Short Tandem Repeats (STRs) from long-read sequencing data
6 versions - Latest release: 12 months ago - 45 downloads last month - 15 stars on GitHub - 2 maintainers
sars2seq 0.1.0
Python library and scripts for working with SARS-CoV-2 sequences.
7 versions - Latest release: about 2 years ago - 1 dependent repositories - 23 downloads last month - 2 stars on GitHub - 1 maintainer
opentargets-checkomatic 0.2.5
This package handles the Open Targets data checking.
9 versions - Latest release: over 5 years ago - 1 dependent repositories - 66 downloads last month - 1 stars on GitHub - 2 maintainers
pxblat 1.1.20
A native python binding for blat suite
25 versions - Latest release: 3 months ago - 481 downloads last month - 10 stars on GitHub - 2 maintainers
seqann 1.0.0
Sequence Annotation
44 versions - Latest release: over 5 years ago - 1 dependent package - 1 dependent repositories - 203 downloads last month - 5 stars on GitHub - 2 maintainers
drep 3.5.0
De-replication of microbial genomes assembled from multiple samples
63 versions - Latest release: 2 months ago - 1 dependent repositories - 545 downloads last month - 234 stars on GitHub - 1 maintainer
Top 7.2% on pypi.org
grakel-dev 0.1a6
A scikit-learn compatible library for graph kernels
5 versions - Latest release: over 4 years ago - 6 dependent repositories - 251 downloads last month - 557 stars on GitHub - 1 maintainer
bio-transformers 0.1.17
Wrapper on top of ESM/Protbert model in order to easily work with protein embedding
28 versions - Latest release: about 2 years ago - 1 dependent repositories - 230 downloads last month - 131 stars on GitHub - 2 maintainers
Top 5.8% on pypi.org
plantcv 4.2.1
An image processing package for plant phenotyping.
33 versions - Latest release: 4 months ago - 25 dependent repositories - 2.5 thousand downloads last month - 612 stars on GitHub - 1 maintainer
de-toolkit 0.9.12
Suite of tools for working with count data
29 versions - Latest release: over 4 years ago - 1 dependent repositories - 169 downloads last month - 2 maintainers
preqc-lr 1.2
Quality control tool for long read sequencing data
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 18 downloads last month - 4 stars on GitHub - 2 maintainers
deepinteract 1.0.9
A geometric deep learning pipeline for predicting protein interface contacts.
9 versions - Latest release: over 2 years ago - 1 dependent repositories - 41 downloads last month - 52 stars on GitHub - 2 maintainers
Top 6.9% on pypi.org
cogent3 2024.2.5a1
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems ...
20 versions - Latest release: 3 months ago - 2 dependent packages - 5 dependent repositories - 1.66 thousand downloads last month - 93 stars on GitHub - 1 maintainer
senseppi 0.7.1
SENSE-PPI: Sequence-based EvolutioNary ScalE Protein-Protein Interaction prediction
17 versions - Latest release: 15 days ago - 208 downloads last month - 1,259 stars on GitHub - 1 maintainer
mygfa 0.1
Simple GFA parsing, printing, and pre-processing in Python.
1 version - Latest release: about 1 month ago - 34 downloads last month - 24 stars on GitHub - 2 maintainers
pycomplexheatmap 1.7.3 💰
A python package to plot complex heatmap
44 versions - Latest release: 7 days ago - 1.7 thousand downloads last month - 232 stars on GitHub - 1 maintainer
dumpling 0.1.3
DUMPLING: command-line app controller
1 version - Latest release: almost 8 years ago - 2 dependent repositories - 19 downloads last month - 0 stars on GitHub - 2 maintainers
versionpy 0.4.11
Small utility to track and bump the version of your python tool
6 versions - Latest release: almost 4 years ago - 4 dependent repositories - 56 downloads last month - 1 stars on GitHub - 2 maintainers
samcc-turbo 0.0.2
Software for automatic detection and measurement of coiled coils in PDB structures.
1 version - Latest release: over 3 years ago - 1 dependent repositories - 13 downloads last month - 3 stars on GitHub - 2 maintainers
mgkit 0.5.8
Metagenomics Framework
30 versions - Latest release: over 2 years ago - 2 dependent repositories - 147 downloads last month - 12 stars on GitHub - 2 maintainers
cpg-workflows 1.23.2
CPG workflows for Hail Batch
98 versions - Latest release: about 14 hours ago - 1 dependent repositories - 6.14 thousand downloads last month - 0 stars on GitHub - 2 maintainers
checkbed 0.2.8
A class for checking plink bed files
6 versions - Latest release: over 9 years ago - 2 dependent repositories - 21 downloads last month - 1 stars on GitHub - 2 maintainers
zfq 1.0.0
FastQ file compressor
1 version - Latest release: 3 months ago - 56 downloads last month - 0 stars on GitHub - 2 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 1 month ago - 40 dependent packages - 166 dependent repositories - 7.79 thousand downloads last month - 838 stars on GitHub - 7 maintainers
aphylogeo 1.0.0
A phylogenetic and geographic analysis tool
7 versions - Latest release: 5 months ago - 56 downloads last month - 9 stars on GitHub - 2 maintainers
autofeather-dash 2.14.2 💰
A Python framework for building reactive web-apps. Developed by Plotly.
4 versions - Latest release: 5 months ago - 36 downloads last month - 20,528 stars on GitHub - 2 maintainers
Top 0.3% on pypi.org
dash 2.16.1 💰
A Python framework for building reactive web-apps. Developed by Plotly.
177 versions - Latest release: about 2 months ago - 294 dependent packages - 11,467 dependent repositories - 2.81 million downloads last month - 20,528 stars on GitHub - 5 maintainers
aprile 0.1.0
Adverse Polypharmacy Reaction Intelligent Learner and Explainer (APRILE) -- An explainable machin...
1 version - Latest release: over 2 years ago - 1 dependent repositories - 29 downloads last month - 7 stars on GitHub - 1 maintainer
cpg-utils 5.0.8
Library of convenience functions specific to the CPG
100 versions - Latest release: 1 day ago - 3 dependent repositories - 4.79 thousand downloads last month - 0 stars on GitHub - 2 maintainers
rpbp 3.0.4
Rp-Bp: Ribosome Profiling with Bayesian Predictions
5 versions - Latest release: about 2 months ago - 1 dependent package - 119 downloads last month - 7 stars on GitHub - 1 maintainer
sphae 1.31
Assembling pure culture phages from both Illumina and Nanopore sequencing technology
4 versions - Latest release: 5 months ago - 23 downloads last month - 13 stars on GitHub - 1 maintainer
metamist 6.10.1
Python API for interacting with the Sample API system
23 versions - Latest release: 2 days ago - 1 dependent repositories - 1.38 thousand downloads last month - 0 stars on GitHub - 2 maintainers
oncopipe 1.0.11
Functions for running Snakemake modules
11 versions - Latest release: over 3 years ago - 1 dependent repositories - 106 downloads last month - 15 stars on GitHub - 1 maintainer
pdbx2df 0.6.7
Super lightweight and fast mmCIF/PDB/MOL2 file parser into Pandas DataFrames and backwards writer.
22 versions - Latest release: 7 months ago - 183 downloads last month - 7 stars on GitHub - 1 maintainer
sam-alignment-reconstructor 0.0.5
SAM Alignment Reconstructor
3 versions - Latest release: almost 6 years ago - 1 dependent repositories - 5 downloads last month - 0 stars on GitHub - 4 maintainers
wbuild 1.8.0
Automatic build tool for R Reports
13 versions - Latest release: over 3 years ago - 1 dependent repositories - 47 downloads last month - 4 stars on GitHub - 2 maintainers
Top 2.9% on pypi.org
dgllife 0.3.2
DGL-based package for Life Science
17 versions - Latest release: about 1 year ago - 5 dependent packages - 29 dependent repositories - 18.1 thousand downloads last month - 684 stars on GitHub - 1 maintainer
cutseq 0.0.34 💰
Automatically cut adapter / barcode / UMI from NGS data
34 versions - Latest release: 1 day ago - 2.34 thousand downloads last month - 3 stars on GitHub - 2 maintainers
camlhmp 0.1.0
Classification through yAML Heuristic Mapping Protocol
2 versions - Latest release: 3 days ago - 270 downloads last month - 1 stars on GitHub - 1 maintainer
Top 9.2% on pypi.org
calour 2019.5.1
CALOUR: exploratory and interactive microbiome analyses based on heatmap
3 versions - Latest release: almost 2 years ago - 2 dependent packages - 4 dependent repositories - 102 downloads last month - 26 stars on GitHub - 1 maintainer
Top 4.1% on pypi.org
harmonypy 0.0.9
A data integration algorithm.
8 versions - Latest release: over 1 year ago - 15 dependent packages - 16 dependent repositories - 9.71 thousand downloads last month - 175 stars on GitHub - 1 maintainer
Top 4.9% on pypi.org
pytabix 0.0.2
Python interface for tabix
2 versions - Latest release: about 9 years ago - 10 dependent packages - 54 dependent repositories - 1.26 thousand downloads last month - 82 stars on GitHub - 2 maintainers
rust-sasa-python 0.1.0
An ultra-fast package for computing Solvent Accessible Surface Area (SASA/ASA) for proteins
1 version - Latest release: 6 days ago - 1.33 thousand downloads last month - 3 stars on GitHub - 2 maintainers
vcftoolz 1.2.3
Tools for working with Variant Call Format files.
7 versions - Latest release: 11 months ago - 1 dependent repositories - 125 downloads last month - 8 stars on GitHub - 4 maintainers
vfind 0.1.0
A simple variant finder for NGS data
1 version - Latest release: 18 days ago - 82 downloads last month - 1 stars on GitHub - 2 maintainers
hyphy 0.1.3
HyPhy package interface library
2 versions - Latest release: over 7 years ago - 1 dependent repositories - 8 downloads last month - 194 stars on GitHub - 2 maintainers
Top 7.5% on pypi.org
hyphy-python 0.1.11
HyPhy package interface library
8 versions - Latest release: 12 months ago - 1 dependent package - 2 dependent repositories - 176 downloads last month - 194 stars on GitHub - 3 maintainers
pegasus-wms.dax 5.0.7
Pegasus Workflow Management System Python API
8 versions - Latest release: 2 months ago - 58 downloads last month - 176 stars on GitHub - 2 maintainers
Top 4.1% on pypi.org
pegasus-wms.api 5.0.7
Pegasus Workflow Management System Python API
8 versions - Latest release: 2 months ago - 1 dependent package - 14 dependent repositories - 15.5 thousand downloads last month - 176 stars on GitHub - 2 maintainers
Top 9.0% on pypi.org
pegasus-wms 5.0.7
Pegasus Workflow Management System Python Codebase
8 versions - Latest release: 2 months ago - 1 dependent package - 11 dependent repositories - 71 downloads last month - 176 stars on GitHub - 3 maintainers
Top 5.4% on pypi.org
pegasus-wms.common 5.0.7
Pegasus Workflow Management System Python Commons
8 versions - Latest release: 2 months ago - 6 dependent repositories - 15.4 thousand downloads last month - 176 stars on GitHub - 4 maintainers
pegasus-wms.worker 5.0.7
Pegasus Workflow Management System Worker Package Tools
8 versions - Latest release: 2 months ago - 2 dependent repositories - 71 downloads last month - 176 stars on GitHub - 2 maintainers
prophyle 0.1.0
ProPhyle metagenomic classifier
54 versions - Latest release: about 7 years ago - 1 dependent repositories - 918 downloads last month - 31 stars on GitHub - 2 maintainers
mda-learn 0.1.1
Manifold Discovery and Analysis (MDA) algorithm for deep learning feature space analysis.
2 versions - Latest release: 5 months ago - 14 downloads last month - 11 stars on GitHub - 2 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: 3 months ago - 17 dependent packages - 166 dependent repositories - 116 thousand downloads last month - 564 stars on GitHub - 4 maintainers
disembl 2.0rc0
A refactoring/reimplementation of DisEMBL
1 version - Latest release: over 7 years ago - 1 dependent repositories - 8 downloads last month - 0 stars on GitHub - 2 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: 8 months ago - 7 dependent packages - 11 dependent repositories - 3.3 thousand downloads last month - 34 stars on GitHub - 6 maintainers
gen3-tracker 0.0.2
Commons utilities
20 versions - Latest release: 28 days ago - 692 downloads last month - 1 stars on GitHub - 6 maintainers
gen3-util 0.0.16
Commons utilities
61 versions - Latest release: 3 months ago - 548 downloads last month - 1 stars on GitHub - 4 maintainers
g3t-etl 0.0.1rc11
Commons utilities
11 versions - Latest release: about 1 month ago - 109 downloads last month - 1 stars on GitHub - 4 maintainers
Top 2.1% on pypi.org
mappy 2.28
Minimap2 python binding
29 versions - Latest release: about 1 month ago - 22 dependent packages - 49 dependent repositories - 4.84 thousand downloads last month - 1,689 stars on GitHub - 1 maintainer