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
sgtree 0.0.10
Computational pipeline for fast and easy construction of phylogenetic trees.1 version - Latest release: almost 4 years ago - 1 dependent repositories - 5 downloads last month - 1 maintainer
dajin2 0.4.6
One-step genotyping tools for targeted long-read sequencing46 versions - Latest release: 5 days ago - 405 downloads last month - 4 stars on GitHub - 1 maintainer
metamist 6.10.2
Python API for interacting with the Sample API system25 versions - Latest release: 14 days ago - 1 dependent repositories - 1.66 thousand downloads last month - 0 stars on GitHub - 1 maintainer
pyfastani 0.5.1
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estima...10 versions - Latest release: 3 months ago - 1 dependent repositories - 616 downloads last month - 14 stars on GitHub - 1 maintainer
msbuddy 0.3.7
Molecular formula annotation for MS-based small molecule analysis.21 versions - Latest release: 2 months ago - 97 downloads last month - 14 stars on GitHub - 1 maintainer
binning-refiner 1.4.3
Binning_refiner4 versions - Latest release: over 3 years ago - 1 dependent repositories - 48 downloads last month - 30 stars on GitHub - 1 maintainer
rose2 1.1.0
ROSE2 python package4 versions - Latest release: over 4 years ago - 2 dependent repositories - 47 downloads last month - 11 stars on GitHub - 4 maintainers
thera-py 0.4.0
VICC normalization routine for therapies34 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
bedshift 1.1.1
BED file perturbations4 versions - Latest release: about 3 years ago - 1 dependent repositories - 31 downloads last month - 3 maintainers
disease-normalizer 0.3.1
VICC normalization routine for diseases26 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
arteria 1.1.4
Helper classes for the arteria project3 versions - Latest release: almost 2 years ago - 1 dependent repositories - 42 downloads last month - 2 maintainers
spsearch 0.1.0 💰
Python tools to get species data from various API.1 version - Latest release: about 5 years ago - 1 dependent repositories - 9 downloads last month - 3 stars on GitHub - 1 maintainer
rbp 0.1.2
Python utils of RBP Bioinformatics.3 versions - Latest release: over 4 years ago - 1 dependent repositories - 20 downloads last month - 1 maintainer
pydstool 0.91.0
Python dynamical systems simulation and modeling4 versions - Latest release: over 4 years ago - 2 dependent repositories - 237 downloads last month - 167 stars on GitHub - 2 maintainers
redundans 0.13a5
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.6 versions - Latest release: over 7 years ago - 1 dependent repositories - 51 downloads last month - 107 stars on GitHub - 1 maintainer
sequencelib 2.20.0
Read, write, and analyze biological sequences32 versions - Latest release: 5 months ago - 4 dependent packages - 1 dependent repositories - 318 downloads last month - 0 stars on GitHub - 1 maintainer
glytrait 0.2.3
A tool for calculating derived traits for N-glycome7 versions - Latest release: 12 months ago - 399 downloads last month - 0 stars on GitHub - 1 maintainer
jonwestern 0.0.1
Spectral Icoshift updated for python v.31 version - Latest release: over 3 years ago - 1 dependent repositories - 3 downloads last month - 0 stars on GitHub - 1 maintainer
Top 3.0% on pypi.org
73 versions - Latest release: over 1 year ago - 7 dependent packages - 34 dependent repositories - 35.2 thousand downloads last month - 232 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 - 35.2 thousand downloads last month - 232 stars on GitHub - 2 maintainers
kcollections 1.0.5
A BloomFilterTrie implementation to be generally applicable for genomic applications.4 versions - Latest release: over 4 years ago - 1 dependent repositories - 75 downloads last month - 2 stars on GitHub - 2 maintainers
counhto 1.1.0
Python package for generating and demultiplexing hash tag oligo count matrices from cellranger ou...2 versions - Latest release: about 1 year ago - 17 downloads last month - 0 stars on GitHub - 1 maintainer
pynteny 0.0.2 removed
Multiple HMM - search via synteny structures in Python1 version - Latest release: over 1 year ago - 20 downloads last month - 5 stars on GitHub
taxpasta 0.6.1
TAXonomic Profile Aggregation and STAndardisation12 versions - Latest release: 8 months ago - 98 downloads last month - 27 stars on GitHub - 3 maintainers
physcraper 1.0.0
Physcraper7 versions - Latest release: over 2 years ago - 1 dependent repositories - 37 downloads last month - 12 stars on GitHub - 1 maintainer
sphae 1.3.3
Assembling pure culture phages from both Illumina and Nanopore sequencing technology7 versions - Latest release: 19 days ago - 299 downloads last month - 17 stars on GitHub - 1 maintainer
cell-blast 0.5.0
Single-cell transcriptome querying tool8 versions - Latest release: over 1 year ago - 84 downloads last month - 1 maintainer
eltetrado 1.5.16
Find and classify tetrads and quadruplexes in DNA/RNA 3D structure38 versions - Latest release: 6 months ago - 1 dependent repositories - 266 downloads last month - 17 stars on GitHub - 1 maintainer
plexlabexchange 0.9.3
A Python interface to the Plex Go CLI.29 versions - Latest release: 9 months ago - 105 downloads last month - 52 stars on GitHub - 2 maintainers
wgse-ng 1.0.0a3
Whole Genome Sequencing data manipulation tool11 versions - Latest release: 4 days ago - 1.31 thousand downloads last month - 2 stars on GitHub - 1 maintainer
pyyamb 0.1.4
Yet Another Metagenome Binner8 versions - Latest release: 8 months ago - 48 downloads last month - 0 stars on GitHub - 1 maintainer
gse 0.1.9
extract metadata and dataset from GEO Series Matrix format data3 versions - Latest release: over 10 years ago - 2 dependent repositories - 27 downloads last month - 1 maintainer
chamredb 0.2.1
Package to find the equivalent antibiotic resistance genes (ARGs) in other databases based on ARG...2 versions - Latest release: over 2 years ago - 25 downloads last month - 113 stars on GitHub - 1 maintainer
xcell 1.1.0.1
Python CLI and module for running the xCell package with Python Pandas inputs and outputs.2 versions - Latest release: over 6 years ago - 1 dependent repositories - 17 downloads last month - 1 stars on GitHub - 1 maintainer
scikit-ribo 0.2.4b1
A scikit framework for joint analysis of Riboseq and RNAseq data1 version - Latest release: almost 7 years ago - 1 dependent repositories - 30 downloads last month - 18 stars on GitHub - 1 maintainer
meta-sparse 0.1.12
SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to pr...12 versions - Latest release: over 5 years ago - 1 dependent repositories - 39 downloads last month - 17 stars on GitHub - 1 maintainer
shortbred 0.9.5
ShortBRED: a system for profiling protein families of interest at very high specificity in shotgu...1 version - Latest release: almost 4 years ago - 1 dependent repositories - 14 downloads last month - 1 maintainer
bio-pype 1.0.7 💰
Management and development framework for bioinformatics pipelines9 versions - Latest release: over 4 years ago - 64 downloads last month - 4,722 stars on GitHub - 1 maintainer
pypop-genomics 1.0.2
PyPop: Python for Population Genomics20 versions - Latest release: 3 months ago - 1.08 thousand downloads last month - 19 stars on GitHub - 1 maintainer
Top 7.3% on pypi.org
20 versions - Latest release: 3 months ago - 1 dependent package - 2 dependent repositories - 871 downloads last month - 342 stars on GitHub - 3 maintainers
histolab 0.7.0 💰
Python library for Digital Pathology Image Processing20 versions - Latest release: 3 months ago - 1 dependent package - 2 dependent repositories - 871 downloads last month - 342 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 thousand downloads last month - 567 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 thousand downloads last month - 567 stars on GitHub - 2 maintainers
mobspy 2.4.4
A Query-Based Language for Chemical Reaction Networks26 versions - Latest release: 4 days ago - 1 dependent repositories - 461 downloads last month - 21 stars on GitHub - 3 maintainers
Top 3.8% on pypi.org
27 versions - Latest release: about 2 months ago - 8 dependent packages - 5 dependent repositories - 247 thousand downloads last month - 163 stars on GitHub - 3 maintainers
bioframe 0.6.4
Operations and utilities for Genomic Interval Dataframes.27 versions - Latest release: about 2 months ago - 8 dependent packages - 5 dependent repositories - 247 thousand downloads last month - 163 stars on GitHub - 3 maintainers
aleph 1.3.1
ALEPH is a bioinformatics tool for structure interpretation and generation of fragment-based libr...17 versions - Latest release: over 3 years ago - 1 dependent repositories - 151 downloads last month - 1 maintainer
detelpy 0.1.13
Python package of the deTEL translation error detection pipeline from mass-spectrometry data9 versions - Latest release: 2 months ago - 59 downloads last month - 108 stars on GitHub - 2 maintainers
fibermorph 0.3.4
Toolkit for analyzing hair fiber morphology22 versions - Latest release: 3 months ago - 1 dependent repositories - 97 downloads last month - 2 stars on GitHub - 2 maintainers
aims-immune 0.9.2
A software for the analysis of immune repertoires16 versions - Latest release: 2 months ago - 88 downloads last month - 9 stars on GitHub - 1 maintainer
vrs-anvil 0.0.1rc2
Commons utilities1 version - Latest release: about 1 month ago - 14 downloads last month - 0 stars on GitHub - 1 maintainer
vrs-anvil-toolkit 0.0.1
Commons utilities1 version - Latest release: about 1 month ago - 13 downloads last month - 0 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 - 25.5 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 - 25.5 thousand downloads last month - 6 stars on GitHub - 1 maintainer
uta-align 0.3.0
C-based sequence alignment for Python21 versions - Latest release: 2 months ago - 3 dependent repositories - 320 downloads last month - 5 stars on GitHub - 2 maintainers
sidr 0.0.2a2
Sequence Idenification using Decision tRees; a tool to classify DNA reads using machine learning ...4 versions - Latest release: almost 6 years ago - 1 dependent repositories - 64 downloads last month - 8 stars on GitHub - 1 maintainer
Top 4.7% on pypi.org
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
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 - 16.2 thousand downloads last month - 35 stars on GitHub - 4 maintainers
amfpy-python 0.1.5
Absolute Molecule File library extension for python1 version - Latest release: 9 months ago - 21 downloads last month - 1 maintainer
bones 0.1
A python toolkit for biology1 version - Latest release: 9 months ago - 2 dependent repositories - 1 maintainer
humann2 2.8.2
HUMAnN2: The HMP Unified Metabolic Analysis Network 225 versions - Latest release: about 4 years ago - 6 dependent repositories - 162 downloads last month - 1 maintainer
bio2bel-mirbase 0.1.1
Convert miRBase to BEL3 versions - Latest release: about 5 years ago - 1 dependent repositories - 55 downloads last month - 0 stars on GitHub - 1 maintainer
pysto 1.4.1
Miscellaneous image processing functions12 versions - Latest release: over 6 years ago - 1 dependent repositories - 109 downloads last month - 4 stars on GitHub - 1 maintainer
scalehd-alspac 0.3
Automated DNA micro-satellite genotyping.1 version - Latest release: about 6 years ago - 1 dependent repositories - 13 downloads last month - 0 stars on GitHub - 1 maintainer
Top 3.2% on pypi.org
80 versions - Latest release: 6 months ago - 21 dependent packages - 40 dependent repositories - 3.27 thousand downloads last month - 327 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 - 3.27 thousand downloads last month - 327 stars on GitHub - 1 maintainer
Top 8.5% on pypi.org
26 versions - Latest release: about 2 months ago - 2 dependent repositories - 605 downloads last month - 295 stars on GitHub - 1 maintainer
truvari 4.2.2
Structural variant comparison tool for VCFs26 versions - Latest release: about 2 months ago - 2 dependent repositories - 605 downloads last month - 295 stars on GitHub - 1 maintainer
Top 4.3% on pypi.org
48 versions - Latest release: 13 days ago - 1 dependent package - 4 dependent repositories - 8.96 thousand downloads last month - 217 stars on GitHub - 4 maintainers
nf-core 2.14.1
Helper tools for use with nf-core Nextflow pipelines.48 versions - Latest release: 13 days ago - 1 dependent package - 4 dependent repositories - 8.96 thousand downloads last month - 217 stars on GitHub - 4 maintainers
profasta 0.0.5
A Python library for working with protein containing FASTA files.5 versions - Latest release: about 1 month ago - 107 downloads last month - 0 stars on GitHub - 1 maintainer
pybedlite 0.0.4 💰
Python classes for interfacing with bed intervals3 versions - Latest release: 8 months ago - 1 dependent repositories - 536 downloads last month - 12 stars on GitHub - 2 maintainers
sequence-align 0.1.1
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms in Rust wit...3 versions - Latest release: 5 days ago - 1 dependent package - 3.04 thousand downloads last month - 58 stars on GitHub - 2 maintainers
pyopencga 3.0.0
A REST client for OpenCGA REST web services61 versions - Latest release: 3 months ago - 1 dependent repositories - 410 downloads last month - 164 stars on GitHub - 2 maintainers
geodb
An asynchronous Python library for the Gene Expression Omnibus (GEO) database1 version - 91 downloads last month - 0 stars on GitHub - 1 maintainer
akrup 1.0.5
Ancestral Karyotype Reconstruction Universal Pipeline6 versions - Latest release: 9 months ago - 55 downloads last month - 2 stars on GitHub - 1 maintainer
probait
Generate target-enrichment probes from a set of genome assemblies.1 version - 0 stars on GitHub
ngsci 0.0.1
The Next Generation Sequencing Complexity Index1 version - Latest release: over 3 years ago - 1 dependent repositories - 13 downloads last month - 0 stars on GitHub - 1 maintainer
rgt 1.0.2
Toolkit to perform regulatory genomics data analysis30 versions - Latest release: 10 months ago - 1 dependent repositories - 299 downloads last month - 100 stars on GitHub - 3 maintainers
stratipy 0.7.2
Patients stratification with Graph-regularized Non-negative Matrix Factorization (GNMF) in Python.4 versions - Latest release: over 6 years ago - 1 dependent repositories - 22 downloads last month - 0 stars on GitHub - 1 maintainer
sctreeshap 0.7.6
sctreeshap: a cluster tree data structure, and for shap analysis31 versions - Latest release: over 2 years ago - 1 dependent repositories - 291 downloads last month - 1 stars on GitHub - 1 maintainer
sevenbridges-cwl 1.1.4
SBG Python library to create CWL tools and workflows5 versions - Latest release: about 3 years ago - 1 dependent repositories - 27 downloads last month - 19 stars on GitHub - 1 maintainer
tiptoft 1.0.2
tiptoft: predict which plasmid should be present from uncorrected long read data6 versions - Latest release: over 4 years ago - 1 dependent repositories - 83 downloads last month - 37 stars on GitHub - 1 maintainer
plasmidpredictor 0.1.0
plasmidpredictor: predict which plasmid should be present from uncorrected long read data1 version - Latest release: over 5 years ago - 1 dependent repositories - 54 downloads last month - 37 stars on GitHub - 1 maintainer
croissance 1.2.0
A tool for estimating growth rates in growth curves.5 versions - Latest release: almost 3 years ago - 30 downloads last month - 24 stars on GitHub - 3 maintainers
biodendro 0.0.3
a package to cluster metabolomics data and plot dendrograms3 versions - Latest release: about 3 years ago - 26 downloads last month - 10 stars on GitHub - 1 maintainer
Top 6.1% on pypi.org
11 versions - Latest release: 3 months ago - 11 dependent packages - 2 dependent repositories - 5.15 thousand downloads last month - 139 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 - 5.15 thousand downloads last month - 139 stars on GitHub - 1 maintainer
bam-readgroup-to-json 0.1
convert each readgroup id to a json file from a BAM24 versions - Latest release: 8 months ago - 1 dependent repositories - 109 downloads last month - 0 stars on GitHub - 1 maintainer
hribo 1.5.0
HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throug...1 version - Latest release: almost 3 years ago - 1 dependent repositories - 9 downloads last month - 8 stars on GitHub - 1 maintainer
graphkb 1.15.0
python adapter for interacting with the GraphKB API21 versions - Latest release: 6 months ago - 1 dependent package - 1 dependent repositories - 112 downloads last month - 7 stars on GitHub - 2 maintainers
Top 7.9% on pypi.org
8 versions - Latest release: about 3 years ago - 1 dependent package - 12 dependent repositories - 140 downloads last month - 49 stars on GitHub - 1 maintainer
plinkio 0.9.8
A library for parsing plink genotype files8 versions - Latest release: about 3 years ago - 1 dependent package - 12 dependent repositories - 140 downloads last month - 49 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
alignqc 2.0.5
Python and R based tool for assessing the quality of alignments2 versions - Latest release: over 6 years ago - 1 dependent repositories - 36 downloads last month - 45 stars on GitHub - 1 maintainer
relecov-tools 0.0.5
Tools for managing and resolution of buisciii services.3 versions - Latest release: over 1 year ago - 2 dependent repositories - 24 downloads last month - 4 stars on GitHub - 1 maintainer
dendropy-calver 2023.330.2
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...1 version - Latest release: about 1 year ago - 13 downloads last month - 0 stars on GitHub - 1 maintainer
phylofisher 1.1.1
PhyloFisher is a software package for the creation, analysis, and visualization of phylogenomic d...41 versions - Latest release: about 2 years ago - 1 dependent repositories - 170 downloads last month - 29 stars on GitHub - 1 maintainer
kipoi-veff 0.3.1
kipoi_veff: variant effect prediction plugin for Kipoi9 versions - Latest release: over 4 years ago - 1 dependent repositories - 160 downloads last month - 6 stars on GitHub - 4 maintainers
cpg-workflows 1.24.4
CPG workflows for Hail Batch106 versions - Latest release: 5 days ago - 1 dependent repositories - 3.83 thousand downloads last month - 0 stars on GitHub - 2 maintainers
mass-dawg 1.1.1
A datastructure for efficient storage of mass spectrometry data4 versions - Latest release: almost 4 years ago - 1 dependent repositories - 29 downloads last month - 0 stars on GitHub - 1 maintainer
molbiox 0.0.13
utilities for bioinformatics7 versions - Latest release: over 8 years ago - 2 dependent repositories - 27 downloads last month - 6 stars on GitHub - 1 maintainer
btm 1.1.5
Blood Transcription Modules for transcriptomics analysis5 versions - Latest release: 10 months ago - 86 downloads last month - 8 stars on GitHub - 1 maintainer
covsonar 2.0.0a1
A database-driven system for handling genomic sequences and screening genomic profiles.2 versions - Latest release: almost 2 years ago - 19 downloads last month - 6 stars on GitHub - 2 maintainers
nabo 0.4.1
Python library to perform memory efficient cross-sample cell mapping using single cell transcipto...6 versions - Latest release: over 3 years ago - 1 dependent repositories - 60 downloads last month - 3 stars on GitHub - 1 maintainer
rnaseqlib 0.1
RNA-Seq analysis pipeline1 version - Latest release: 9 months ago - 2 dependent repositories - 1 maintainer
gfunc 0.0.0
[coming soon] gFunc: functional genomics using graphs for integration of many Omics data types1 version - Latest release: 9 months ago - 2 dependent repositories - 1 maintainer
magna 4.1.0
Magna is a collection of commands that I frequently use in bioinformatics and day-to-day life.33 versions - Latest release: over 1 year ago - 1 dependent repositories - 279 downloads last month - 1 stars on GitHub - 1 maintainer
kmer 1.0.2
k-mer analysis toolkit and programming library.5 versions - Latest release: over 9 years ago - 1 dependent repositories - 21 downloads last month - 30 stars on GitHub - 1 maintainer
python-queen 1.1.0
QUEEN (a Python module to universally program, QUinE, and Edit Nucleotide sequences)3 versions - Latest release: almost 2 years ago - 1 dependent repositories - 28 downloads last month - 35 stars on GitHub - 1 maintainer
pymasc 0.3.2
Python implementation to calc mappability-sensitive cross-correlation for fragment length estimat...12 versions - Latest release: over 4 years ago - 1 dependent repositories - 37 downloads last month - 2 stars on GitHub - 1 maintainer
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