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 2.0% on pypi.org
multiqc 1.22.1
Create aggregate bioinformatics analysis reports across many samples and tools
37 versions - Latest release: 15 days ago - 7 dependent packages - 74 dependent repositories - 12.3 thousand downloads last month - 1,162 stars on GitHub - 1 maintainer
gpml2svg 0.3.0
Render GPML pathway markup to SVG from the commandline/Python.
11 versions - Latest release: almost 10 years ago - 2 dependent repositories - 40 downloads last month - 1 stars on GitHub - 1 maintainer
efishent 0.0.5
RNA FISH oligos/probes design tool.
5 versions - Latest release: 12 months ago - 32 downloads last month - 10 stars on GitHub - 1 maintainer
fdstools 2.0.4
Forensic DNA Sequencing Tools
14 versions - Latest release: over 1 year ago - 2 dependent repositories - 610 downloads last month - 5 stars on GitHub - 1 maintainer
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 - 20 downloads last month - 4 stars on GitHub - 5 maintainers
datasnakes 0.1.1a1
This package helps in the analysis of orthologous genes.
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 5 downloads last month - 27 stars on GitHub - 1 maintainer
njab 0.0.6
not Just Another Biomarker
8 versions - Latest release: 18 days ago - 1 dependent package - 1.93 thousand downloads last month - 1 maintainer
Top 9.0% on pypi.org
gencove 2.16.3
Gencove API and CLI tool
123 versions - Latest release: 23 days ago - 1 dependent repositories - 57.8 thousand downloads last month - 4 stars on GitHub - 1 maintainer
pyfilo 0.0.1
Python library for handling bioinformatics data
1 version - Latest release: 10 months ago - 4 downloads last month - 1 maintainer
seq-experiment 0.1.2
3 versions - Latest release: over 6 years ago - 1 dependent repositories - 14 downloads last month - 1 maintainer
smallbixtools 0.0.34
A few small methods for bioinformatics
20 versions - Latest release: about 4 years ago - 1 dependent repositories - 63 downloads last month - 2 maintainers
Top 6.9% on pypi.org
basepair 2.1.1
Python client for Basepair's API
85 versions - Latest release: about 1 month ago - 2 dependent repositories - 78.2 thousand downloads last month - 6 maintainers
cgt 0.3.1
Tools for representing genomes in sage
17 versions - Latest release: 11 months ago - 1 dependent repositories - 126 downloads last month - 1 stars on GitHub - 1 maintainer
primerserver2 2.0.0b20
a high-throughput primer design and specificity-checking platform
23 versions - Latest release: over 2 years ago - 1 dependent repositories - 108 downloads last month - 69 stars on GitHub - 1 maintainer
motifscan 1.3.0
A package for motif discovery and motif enrichment analysis
6 versions - Latest release: over 3 years ago - 1 dependent repositories - 39 downloads last month - 18 stars on GitHub - 1 maintainer
pocketutils 0.9.1
Adorable little Python code for you to copy or import.
21 versions - Latest release: almost 2 years ago - 1 dependent repositories - 86 downloads last month - 2 stars on GitHub - 1 maintainer
Top 1.7% on pypi.org
dendropy 4.6.1
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...
27 versions - Latest release: 12 months ago - 33 dependent packages - 109 dependent repositories - 6.85 thousand downloads last month - 3 maintainers
trailblazer 21.5.15
Trailblazer is a tool to manage and track state of analyses
269 versions - Latest release: 17 days ago - 1 dependent package - 1 dependent repositories - 2.44 thousand downloads last month - 5 stars on GitHub - 5 maintainers
fastlmmclib 0.0.3
Fast GWAS C library
3 versions - Latest release: 10 months ago - 2 dependent packages - 1 dependent repositories - 522 downloads last month - 0 stars on GitHub - 1 maintainer
Top 6.9% on pypi.org
bionumpy 1.0.8
Library for working with biological sequence data as numpy arrays.
44 versions - Latest release: 3 months ago - 5 dependent packages - 5 dependent repositories - 1.28 thousand downloads last month - 84 stars on GitHub - 1 maintainer
pynteny 0.0.2 removed
Multiple HMM - search via synteny structures in Python
1 version - Latest release: over 1 year ago - 20 downloads last month - 5 stars on GitHub
tidytcells 2.1.1
Standardise TR/MH data
33 versions - Latest release: 3 months ago - 2 dependent packages - 1 dependent repositories - 184 downloads last month - 4 stars on GitHub - 1 maintainer
taxpasta 0.6.1
TAXonomic Profile Aggregation and STAndardisation
12 versions - Latest release: 8 months ago - 76 downloads last month - 27 stars on GitHub - 3 maintainers
physcraper 1.0.0
Physcraper
7 versions - Latest release: over 2 years ago - 1 dependent repositories - 34 downloads last month - 12 stars on GitHub - 1 maintainer
geneview 0.2.1
Geneview: A python package for genomics data visualization.
22 versions - Latest release: 12 months ago - 1 dependent package - 2 dependent repositories - 126 downloads last month - 58 stars on GitHub - 1 maintainer
kipoi-interpret 0.1.2
Kipoi interpret: interepretation plugin for Kipoi
3 versions - Latest release: over 5 years ago - 1 dependent repositories - 292 downloads last month - 3 stars on GitHub - 4 maintainers
barrnap 0.0.5
python package for barrnap
7 versions - Latest release: over 6 years ago - 1 dependent repositories - 38 downloads last month - 1 maintainer
mah51-biopython 1.1
Freely available tools for computational molecular biology.
2 versions - Latest release: about 2 years ago - 1 dependent repositories - 19 downloads last month - 3,900 stars on GitHub - 1 maintainer
driven 0.0.3
driven - data-driven constraint-based analysis
5 versions - Latest release: over 7 years ago - 7 dependent repositories - 29 downloads last month - 3 maintainers
rcgrep 0.1.0
Search text files for DNA sequences and their reverse complements
3 versions - Latest release: about 7 years ago - 1 dependent repositories - 13 downloads last month - 6 stars on GitHub - 1 maintainer
jobrunner 1.4.0
An abstraction layer to run jobs on HPC clusters using Grid Engine, Torque, or locally.
6 versions - Latest release: almost 4 years ago - 1 dependent repositories - 51 downloads last month - 2 stars on GitHub - 2 maintainers
simplebitk 0.0.1a0
A bioinformatics tools kit
1 version - Latest release: over 3 years ago - 1 dependent repositories - 18 downloads last month - 0 stars on GitHub - 1 maintainer
optipyzer 0.4.1
Codon optimize DNA and Protein sequences for multiple species.
8 versions - Latest release: over 1 year ago - 1 dependent repositories - 66 downloads last month - 22 stars on GitHub - 1 maintainer
better-fasta-grep 1.0.4
Grep-like tool for retrieving matching sequence records from a FASTA file
5 versions - Latest release: about 1 year ago - 1 dependent repositories - 46 downloads last month - 3 stars on GitHub - 2 maintainers
mutalyzer 3.0.7
Mutalyzer HGVS variant description tools.
9 versions - Latest release: 4 months ago - 1 dependent package - 1 dependent repositories - 52 downloads last month - 29 stars on GitHub - 1 maintainer
arv 0.9.2
A fast 23andMe raw genome file parser
11 versions - Latest release: about 7 years ago - 139 downloads last month - 114 stars on GitHub - 1 maintainer
clinvar-this 0.14.6
ClinVar Submission via API Made Easy
29 versions - Latest release: 6 months ago - 408 downloads last month - 6 stars on GitHub - 1 maintainer
plassembler 1.6.2
Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates
10 versions - Latest release: 3 months ago - 54 downloads last month - 45 stars on GitHub - 1 maintainer
compath-hgnc 0.0.2
A package that wraps PyHGNC to perform mappings between different gene identifiers
2 versions - Latest release: almost 6 years ago - 19 downloads last month - 0 stars on GitHub - 2 maintainers
cisvar 2.0.0b3
Calculate both pre and post frequencies for ChIP or ATAC style data
1 version - Latest release: about 6 years ago - 14 downloads last month - 5 stars on GitHub - 1 maintainer
sequencetools 0.0.7
sequencetools -- A package for FASTX stats generation and manipulation
7 versions - Latest release: over 4 years ago - 1 dependent repositories - 39 downloads last month - 2 stars on GitHub - 1 maintainer
icoshift 1.0
icoshift: A versatile tool for the rapid alignment of 1D NMR spectra
8 versions - Latest release: over 9 years ago - 2 dependent repositories - 49 downloads last month - 15 stars on GitHub - 1 maintainer
vcf2networks 1.0.8
calculate Genotype Networks from VCF files
18 versions - Latest release: over 10 years ago - 2 dependent repositories - 191 downloads last month - 1 maintainer
msexpert 0.0.2
An open-source Python package of the AlphaPept ecosystem
2 versions - Latest release: over 2 years ago - 1 dependent repositories - 15 downloads last month - 1 maintainer
isambard 2.3.1
A package for biomolecular analysis, modelling and design
3 versions - Latest release: about 3 years ago - 2 dependent repositories - 25 downloads last month - 20 stars on GitHub - 3 maintainers
sigalign 0.2.0
SigAlign's language binding for python
2 versions - Latest release: 11 months ago - 16 downloads last month - 10 stars on GitHub - 1 maintainer
nanosim-h 1.1.0.4
NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
5 versions - Latest release: almost 6 years ago - 1 dependent repositories - 25 downloads last month - 16 stars on GitHub - 1 maintainer
umitools 0.3.4
A toolset for handling sequencing data with unique molecular identifiers (UMIs)
3 versions - Latest release: about 6 years ago - 2 dependent repositories - 64 downloads last month - 12 stars on GitHub - 1 maintainer
geofetch 0.12.6
Downloads data and metadata from GEO and SRA and creates standard PEPs.
22 versions - Latest release: 4 months ago - 1 dependent repositories - 384 downloads last month - 40 stars on GitHub - 3 maintainers
probabilistic2020 1.2.3
Probabilistic 20/20
14 versions - Latest release: almost 5 years ago - 4 dependent repositories - 62 downloads last month - 8 stars on GitHub - 1 maintainer
Top 7.1% on pypi.org
ariba 2.14.6
ARIBA: Antibiotic Resistance Identification By Assembly
53 versions - Latest release: over 3 years ago - 7 dependent repositories - 485 downloads last month - 154 stars on GitHub - 1 maintainer
qubekit 2.6.3
Quantum mechanical bespoke force field parameter generation
12 versions - Latest release: over 4 years ago - 1 dependent repositories - 84 downloads last month - 91 stars on GitHub - 1 maintainer
Top 9.4% on pypi.org
staramr 0.10.0
Scans genome contigs against ResFinder, PlasmidFinder, and PointFinder databases
18 versions - Latest release: 9 months ago - 4 dependent repositories - 279 downloads last month - 96 stars on GitHub - 2 maintainers
ngs-chew 0.9.4
NGS Chew
11 versions - Latest release: 3 months ago - 40 downloads last month - 2 stars on GitHub - 1 maintainer
sato 0.1.7
Python package that generates consensus sequence from the forward and reverse sequences, performs...
9 versions - Latest release: about 1 month ago - 69 downloads last month - 0 stars on GitHub - 1 maintainer
seqshannon 1.0.0
Calculate shannon entropy of biological sequences
1 version - Latest release: 10 months ago - 19 downloads last month - 3 stars on GitHub - 1 maintainer
oldowan.mtconvert 1.0.6
Transform human mtDNA sequence to variant sites and vice versa.
5 versions - Latest release: almost 9 years ago - 3 dependent repositories - 13 downloads last month - 1 maintainer
xebec 0.5.1
Snakemake pipeline for microbiome diversity effect size benchmarking.
2 versions - Latest release: almost 2 years ago - 1 dependent repositories - 51 downloads last month - 5 stars on GitHub - 1 maintainer
Top 5.4% on pypi.org
pegasus-wms.common 5.0.7
Pegasus Workflow Management System Python Commons
8 versions - Latest release: 3 months ago - 6 dependent repositories - 11.8 thousand downloads last month - 177 stars on GitHub - 2 maintainers
pegasus-wms.dax 5.0.7
Pegasus Workflow Management System Python API
8 versions - Latest release: 3 months ago - 50 downloads last month - 177 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: 3 months ago - 1 dependent package - 14 dependent repositories - 11.9 thousand downloads last month - 177 stars on GitHub - 2 maintainers
pegasus-wms.worker 5.0.7
Pegasus Workflow Management System Worker Package Tools
8 versions - Latest release: 3 months ago - 2 dependent repositories - 47 downloads last month - 177 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: 3 months ago - 1 dependent package - 11 dependent repositories - 60 downloads last month - 176 stars on GitHub - 3 maintainers
Top 6.6% on pypi.org
dash-tools 1.12.0 💰
Plotly Dash Templating and Deployment Tools
48 versions - Latest release: 8 months ago - 40 dependent repositories - 2.3 thousand downloads last month - 92 stars on GitHub - 1 maintainer
pypop-genomics 1.0.2
PyPop: Python for Population Genomics
22 versions - Latest release: 3 months ago - 880 downloads last month - 19 stars on GitHub - 1 maintainer
bio-jtools 0.2.3
Various bioinformatics tools in one package
4 versions - Latest release: over 4 years ago - 1 dependent repositories - 40 downloads last month - 0 stars on GitHub - 1 maintainer
clumps-ptm 0.0.6
CLUMPS-PTM driver gene discovery using 3D protein structure (Getz Lab).
7 versions - Latest release: about 1 year ago - 29 downloads last month - 6 stars on GitHub - 1 maintainer
orthomap 0.0.1
extract orthomap from OrthoFinder output for query species
1 version - Latest release: about 1 year ago - 7 downloads last month - 6 stars on GitHub - 1 maintainer
rafm 1.1.4
rafm
10 versions - Latest release: over 2 years ago - 1 dependent repositories - 47 downloads last month - 1 stars on GitHub - 1 maintainer
ntmirror 1.4.1
Easily updatable local NCBI taxonomy database copy
6 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 44 downloads last month - 4 stars on GitHub - 1 maintainer
ngs_utils 2.3.16
Utils for NGS pipelines by Vlad Saveliev
9 versions - Latest release: over 5 years ago - 1 dependent repositories - 44 downloads last month - 2 stars on GitHub - 1 maintainer
aaindex 1.1.2
A lightweight Python software package for accessing the data in the various AAIndex databases, wh...
10 versions - Latest release: 7 months ago - 3 dependent packages - 1 dependent repositories - 311 downloads last month - 7 stars on GitHub - 1 maintainer
flatgfa 0.1.3
efficient processing of pangenomes in Graphical Fragment Assembly (GFA) format
2 versions - Latest release: 16 days ago - 436 downloads last month - 24 stars on GitHub - 1 maintainer
mygfa 0.1
Simple GFA parsing, printing, and pre-processing in Python.
1 version - Latest release: 2 months ago - 16 downloads last month - 24 stars on GitHub - 1 maintainer
g3t-etl 0.0.1rc11
Commons utilities
17 versions - Latest release: 2 months ago - 414 downloads last month - 1 stars on GitHub - 3 maintainers
gen3-util 0.0.16
Commons utilities
61 versions - Latest release: 4 months ago - 227 downloads last month - 1 stars on GitHub - 3 maintainers
pyrcos 0.0.1
Python hi-level interface for circos
2 versions - Latest release: 9 months ago - 2 dependent repositories - 6 downloads last month - 1 maintainer
mspect 0.0.1
TODO
1 version - Latest release: 4 months ago - 5 downloads last month - 1 maintainer
seqvec 0.4.1
Embeeder tool for 'Modelling the Language of Life - Deep Learning Protein Sequences'
6 versions - Latest release: almost 4 years ago - 1 dependent package - 1 dependent repositories - 92 downloads last month - 110 stars on GitHub - 1 maintainer
entrezpy 2.1.3
Dedicated library to query and retrieve data from Entrez databases at NCBI
18 versions - Latest release: about 3 years ago - 2 dependent packages - 12 dependent repositories - 680 downloads last month - 3 stars on GitLab.com - 1 maintainer
genepidgin 1.1.1
gene naming utility belt
2 versions - Latest release: almost 12 years ago - 2 dependent repositories - 11 downloads last month - 1 maintainer
nextflowpy 0.8.1
A Python wrapper around Nextflow.
21 versions - Latest release: 7 months ago - 2.5 thousand downloads last month - 51 stars on GitHub - 1 maintainer
altamisa 0.2.9
Implementation of ISA-tools data model and ISA-TAB
2 versions - Latest release: about 3 years ago - 5 dependent repositories - 709 downloads last month - 5 stars on GitHub - 2 maintainers
biobear 0.20.0 💰
A package for working with Bioinformatics data with SQL and Arrow
53 versions - Latest release: about 1 month ago - 1 dependent package - 6.76 thousand downloads last month - 123 stars on GitHub - 1 maintainer
lpbio 0.1.0a0
lpbio provides scripts and modules for computational biology
1 version - Latest release: over 5 years ago - 1 dependent repositories - 8 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 - 11 downloads last month - 0 stars on GitHub - 1 maintainer
Top 4.7% on pypi.org
dsub 0.4.11
A command-line tool that makes it easy to submit and run batch scripts in the cloud
43 versions - Latest release: 26 days ago - 15 dependent repositories - 12.8 thousand downloads last month - 257 stars on GitHub - 2 maintainers
blockdata 0.3.2
Store coordinate values as a compressed block.
6 versions - Latest release: almost 5 years ago - 39 downloads last month - 1 maintainer
aphylogeo 1.0.0
A phylogenetic and geographic analysis tool
7 versions - Latest release: 6 months ago - 51 downloads last month - 9 stars on GitHub - 1 maintainer
hyphy 0.1.3
HyPhy package interface library
2 versions - Latest release: over 7 years ago - 1 dependent repositories - 5 downloads last month - 198 stars on GitHub - 1 maintainer
samtools_metrics_sqlite 0.6
store samtools metrics in sqlite
6 versions - Latest release: over 6 years ago - 18 downloads last month - 0 stars on GitHub - 1 maintainer
trxtools 0.2.2
Python tools facilitating bioinformatic analysis of nascent transcripts and transcriptomic data.
3 versions - Latest release: over 1 year ago - 18 downloads last month - 2 stars on GitHub - 1 maintainer
Top 4.1% on pypi.org
pyfasta 0.5.2 💰
fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
27 versions - Latest release: about 10 years ago - 4 dependent packages - 57 dependent repositories - 1.89 thousand downloads last month - 86 stars on GitHub - 1 maintainer
gtf_to_genes 1.08
Fast GTF parser
14 versions - Latest release: 9 months ago - 3 dependent repositories - 41 downloads last month - 1 maintainer
pgp-reconstruction 0.1.0
Pathway-Guided Pruning Reconstruction of constraint-based metabolic models
8 versions - Latest release: about 1 year ago - 30 downloads last month - 11 stars on GitHub - 1 maintainer
smasher 1.0
Smash molecule and obtain significant fragments
1 version - Latest release: about 3 years ago - 1 dependent repositories - 11 downloads last month - 16 stars on GitHub - 1 maintainer
finaletoolkit 0.5.2
FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free ...
6 versions - Latest release: 24 days ago - 1 dependent package - 611 downloads last month - 3 stars on GitHub - 1 maintainer
pyjess 0.1.0
Cython bindings and Python interface to JESS, a 3D template matching software.
4 versions - Latest release: about 1 month ago - 461 downloads last month - 2 stars on GitHub - 1 maintainer
moclo-ecoflex 0.3.1
EcoFlex implementation for the base moclo library.
5 versions - Latest release: over 5 years ago - 1 dependent repositories - 15 downloads last month - 12 stars on GitHub - 1 maintainer
Top 6.1% on pypi.org
decoupler 1.6.0
Ensemble of methods to infer biological activities from omics data
11 versions - Latest release: 3 months ago - 11 dependent packages - 2 dependent repositories - 5.33 thousand downloads last month - 141 stars on GitHub - 1 maintainer