Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

pypi.org "genetics" keyword

genegist 0.1.5
Create summararies of groups of genes.
6 versions - Latest release: 5 months ago - 48 downloads last month - 0 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...
28 versions - Latest release: 12 months ago - 33 dependent packages - 109 dependent repositories - 6.94 thousand downloads last month - 3 maintainers
gene-fetchr 1.0.0b0
Search, retrieve, and scrape biological data from annotated genomes or public databases.
1 version - Latest release: over 1 year ago - 12 downloads last month - 1 maintainer
easyae-samuel.revolinski 0.0.0
easy way for non-linear dimensionality increase or reduction
1 version - Latest release: over 5 years ago - 11 downloads last month - 0 stars on GitHub - 1 maintainer
gepyto 0.10.1
Utilities and tools to interface with genomic databases and to facilitate common bioinformatics t...
3 versions - Latest release: over 8 years ago - 3 dependent repositories - 161 downloads last month - 7 stars on GitHub - 1 maintainer
Top 8.2% on pypi.org
fastlmm 0.6.8
Fast GWAS
52 versions - Latest release: about 1 month ago - 1 dependent package - 7 dependent repositories - 535 downloads last month - 43 stars on GitHub - 4 maintainers
wgse-ng 1.0.0a3
Whole Genome Sequencing data manipulation tool
17 versions - Latest release: 16 days ago - 1.74 thousand downloads last month - 2 stars on GitHub - 1 maintainer
Top 8.5% on pypi.org
sgkit 0.8.0
Statistical genetics toolkit
8 versions - Latest release: about 1 month ago - 2 dependent packages - 5 dependent repositories - 1.42 thousand downloads last month - 213 stars on GitHub - 1 maintainer
pyflagstats 0.1.4
Efficient subroutines for computing summary statistics for the SAM FLAG field
5 versions - Latest release: over 4 years ago - 1 dependent repositories - 15 downloads last month - 15 stars on GitHub - 1 maintainer
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: 9 months ago - 1 dependent repositories - 48 downloads last month - 5 stars on GitHub - 1 maintainer
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
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
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
trifusion 1.0.2
Streamlining phylogenomic data gathering, processing and visualization
35 versions - Latest release: over 5 years ago - 1 dependent repositories - 164 downloads last month - 87 stars on GitHub - 1 maintainer
locuspocus 1.1.0
Genetic coordinates made easy!
7 versions - Latest release: about 4 years ago - 4 dependent repositories - 23 downloads last month - 10 stars on GitHub - 1 maintainer
genipe 1.5.0
An automatic genome-wide imputation pipeline.
13 versions - Latest release: over 3 years ago - 3 dependent repositories - 81 downloads last month - 30 stars on GitHub - 1 maintainer
genbank-download 0.5
a small script to download nucleotide sequences from genbank using an accession number.
1 version - Latest release: over 14 years ago - 2 dependent repositories - 15 downloads last month - 1 maintainer
hybkit 0.3.3
Toolkit for analysis of chimeric (hybrid) RNA sequence data.
6 versions - Latest release: 9 months ago - 1 dependent repositories - 35 downloads last month - 8 stars on GitHub - 1 maintainer
Top 8.8% on pypi.org
limix 3.0.4
Genetic analysis toolbox using mixed models
90 versions - Latest release: over 4 years ago - 6 dependent repositories - 372 downloads last month - 97 stars on GitHub - 2 maintainers
cutevariant 0.4.5 💰
GUI to visualize and process variant data
36 versions - Latest release: about 1 year ago - 1 dependent repositories - 152 downloads last month - 89 stars on GitHub - 2 maintainers
pydigree 1.0.1
A package for operations on pedigree and genotype data
3 versions - Latest release: over 6 years ago - 1 dependent repositories - 20 downloads last month - 20 stars on GitHub - 1 maintainer
vcfsynonymous 0.2.0
Detect synonymous genetic variants in VCF
18 versions - Latest release: over 3 years ago - 1 dependent repositories - 218 downloads last month - 1 stars on GitHub - 1 maintainer
ponytools 0.2.3
Computational tools that you will ride into the FUTURE.
11 versions - Latest release: about 5 years ago - 3 dependent repositories - 48 downloads last month - 1 stars on GitHub - 1 maintainer
stirplate 1.4.0
Stirplate Data Uploader
5 versions - Latest release: almost 8 years ago - 2 dependent repositories - 36 downloads last month - 0 stars on GitHub - 1 maintainer
variant-extractor 4.0.6
Deterministic and standard extractor of indels, SNVs and structural variants (SVs) from VCF files
6 versions - Latest release: about 1 year ago - 1 dependent package - 27 downloads last month - 3 stars on GitHub - 1 maintainer
buddysuite 1.4.0
BuddySuite is a collection of command line utilities written in Python for working with biologica...
14 versions - Latest release: over 2 years ago - 1 dependent repositories - 69 downloads last month - 121 stars on GitHub - 1 maintainer
ibd-dendrogram 0.12.4
module that helps to form a dendrogram
9 versions - Latest release: 4 months ago - 52 downloads last month - 0 stars on GitHub - 1 maintainer
epistasis 0.7.5
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
17 versions - Latest release: almost 3 years ago - 3 dependent repositories - 98 downloads last month - 32 stars on GitHub - 3 maintainers
evolution-of-algebraic-terms 1.8.7
EAT is software implementation of the algorithms described in the paper Evolution of Algebraic Te...
1 version - Latest release: 3 months ago - 13 downloads last month - 1 stars on GitHub - 1 maintainer
page-enrichment 0.1.4
Parametric Analysis of Gene Set Enrichment (PAGE).
2 versions - Latest release: about 3 years ago - 1 dependent repositories - 21 downloads last month - 0 stars on GitHub - 1 maintainer
lzgraphs 1.0.2
An Implementation of LZ76 Based Graphs for Repertoire Representation and Analysis
11 versions - Latest release: 2 months ago - 43 downloads last month - 4 stars on GitHub - 1 maintainer
gnomad-db 0.1.4
This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. ...
13 versions - Latest release: 7 months ago - 1 dependent repositories - 167 downloads last month - 27 stars on GitHub - 1 maintainer
ibdcluster 1.2.9
A CLI tool to help identify ibd sharing within networks across a locus of interest at biobank sca...
7 versions - Latest release: about 1 year ago - 41 downloads last month - 0 stars on GitHub - 1 maintainer
gpmap 0.7.0
A Python API for managing genotype-phenotype map data
15 versions - Latest release: almost 4 years ago - 7 dependent repositories - 96 downloads last month - 11 stars on GitHub - 3 maintainers
breedgym 0.0.1a0
Suite of Gymnasium environments for optimizing breeding programs
2 versions - Latest release: 6 months ago - 9 downloads last month - 1 stars on GitHub - 1 maintainer
varfish-cli 0.6.3
Command line interface client for VarFish Server.
22 versions - Latest release: 4 months ago - 4 dependent repositories - 288 downloads last month - 2 stars on GitHub - 1 maintainer
vcfio 1.1.9
A simple and efficient VCF manipulation package.
9 versions - Latest release: 4 months ago - 1 dependent repositories - 1.05 thousand downloads last month - 6 stars on GitHub - 1 maintainer
hchacha 1.0.5
Human CHromosome Accession CHAnge - Convert between different human chromosome naming systems (of...
6 versions - Latest release: 11 months ago - 48 downloads last month - 1 maintainer
parett 1.0.1
Python Automated Retrieval of TimeTree data
1 version - Latest release: almost 2 years ago - 11 downloads last month - 1 stars on GitHub - 1 maintainer
moose-classifier 0.9
Alignment based taxonomic classifier
4 versions - Latest release: over 2 years ago - 1 dependent repositories - 28 downloads last month - 0 stars on GitHub - 1 maintainer
tcga 0.0.22
Computational biology & bioinformatics utils
20 versions - Latest release: about 3 years ago - 1 dependent repositories - 150 downloads last month - 3 stars on GitHub - 1 maintainer
gene-normalizer 0.2.10
VICC normalization routine for genes
51 versions - Latest release: 11 months ago - 4 dependent packages - 6 dependent repositories - 1.73 thousand downloads last month - 1 stars on GitHub - 3 maintainers
drive-ibd 2.7.1
cli tool to identify networks of individuals who share IBD segments overlapping loci of interest
34 versions - Latest release: about 1 month ago - 242 downloads last month - 0 stars on GitHub - 2 maintainers
snipar 0.0.18
Library and command line scripts for inferring identity-by-descent (IBD) segments shared between ...
14 versions - Latest release: 11 months ago - 1 dependent repositories - 304 downloads last month - 22 stars on GitHub - 2 maintainers
genome-to-sqlite 0.1
Import your genome into a SQLite database
1 version - Latest release: over 4 years ago - 1 dependent repositories - 5 downloads last month - 20 stars on GitHub - 1 maintainer
geonomics 1.4.1
A package for landscape genomic simulation
70 versions - Latest release: about 1 month ago - 7 dependent repositories - 565 downloads last month - 9 stars on GitHub - 1 maintainer
codons 0.0.10
Translates and transcribes an arbitrary genetic sequence, generates FASTA-formatted files, and in...
10 versions - Latest release: about 2 years ago - 47 downloads last month - 0 stars on GitHub - 1 maintainer
seq-dove 0.4.4
Set of tools for downstream vcf analysis
24 versions - Latest release: over 3 years ago - 1 dependent repositories - 131 downloads last month - 1 maintainer
greatbrowser 0.0.1
Automate Stanford's GREAT browser
8 versions - Latest release: 21 days ago - 1.6 thousand downloads last month - 0 stars on GitHub - 1 maintainer
mutalyzer-algebra 1.5.1
A Boolean Algebra for Genetic Variants
20 versions - Latest release: 5 months ago - 2 dependent packages - 1 dependent repositories - 153 downloads last month - 10 stars on GitHub - 2 maintainers
orthoevol 0.9.0a2
This package aids in the analysis of orthologous genes.
1 version - Latest release: over 6 years ago - 1 dependent repositories - 7 downloads last month - 27 stars on GitHub - 2 maintainers
rnacounter 1.5.2
Estimate abundances of genomic features from read densities
14 versions - Latest release: over 9 years ago - 2 dependent repositories - 59 downloads last month - 1 stars on GitHub - 2 maintainers
bamnostic 1.1.10
Pure Python, OS-agnostic Binary Alignment Map (BAM) random access and parsing tool
54 versions - Latest release: about 1 year ago - 3 dependent packages - 1 dependent repositories - 643 downloads last month - 94 stars on GitHub - 1 maintainer
scbamtools 0.5
High performance Cython + Python tools to process BAM files with tags as they arise in single-cel...
4 versions - Latest release: 3 months ago - 21 downloads last month - 1 stars on GitHub - 1 maintainer
seq-pigeon 0.4.3
Pipeline tool for NGS data
17 versions - Latest release: over 3 years ago - 1 dependent repositories - 35 downloads last month - 942 stars on GitHub - 1 maintainer
warpedlmm 0.21
Warped linear mixed model
7 versions - Latest release: about 9 years ago - 1 dependent repositories - 48 downloads last month - 1 maintainer
Top 7.9% on pypi.org
plinkio 0.9.8
A library for parsing plink genotype files
8 versions - Latest release: over 3 years ago - 1 dependent package - 12 dependent repositories - 140 downloads last month - 49 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
leapdna 0.1.0
A Python 3.9 implementation of the leapdna toolkit
1 version - Latest release: about 3 years ago - 1 dependent repositories - 9 downloads last month - 0 stars on GitHub - 1 maintainer
j11hail 99.2.58
Scalable library for exploring and analyzing genomic data.
4 versions - Latest release: over 3 years ago - 1 dependent repositories - 47 downloads last month - 925 stars on GitHub - 2 maintainers
pysumstats 0.5.2
Package for working with GWAS summary statistics
20 versions - Latest release: over 3 years ago - 1 dependent repositories - 152 downloads last month - 0 stars on GitHub - 1 maintainer
genebe 0.0.18
GeneBe Client: A user-friendly system for annotating genetic variants
15 versions - Latest release: 16 days ago - 330 downloads last month - 1 stars on GitHub - 1 maintainer
cpg-hail 0.2.90
Scalable library for exploring and analyzing genomic data.
6 versions - Latest release: about 2 years ago - 1 dependent repositories - 36 downloads last month - 925 stars on GitHub - 2 maintainers
genrisk 0.3.1
Comprehensive genetic risk assessment
19 versions - Latest release: 7 months ago - 1 dependent repositories - 209 downloads last month - 7 stars on GitHub - 1 maintainer
scarv 0.5
Selective Constraint Against Rare Variants
1 version - Latest release: over 2 years ago - 1 dependent repositories - 12 downloads last month - 0 stars on GitHub - 1 maintainer
bioprot 0.2.0
A package for DNA, RNA and protein sequence manipulation
1 version - Latest release: 16 days ago - 0 stars on GitHub
rrat 0.6
Ribosomal RNA Allele Tree
6 versions - Latest release: about 6 years ago - 1 dependent repositories - 34 downloads last month - 0 stars on GitHub - 1 maintainer
grstools 0.4.0
Tools to manipulate genetic risk scores.
3 versions - Latest release: over 5 years ago - 1 dependent repositories - 49 downloads last month - 4 stars on GitHub - 1 maintainer
cada-prio 0.6.1
Phenotype-based prioritization of variants with CADA
8 versions - Latest release: 7 months ago - 26 downloads last month - 0 stars on GitHub - 1 maintainer
vencode 1.2.0
Package to get VEnCodes as in Macedo and Gontijo, 2019
18 versions - Latest release: over 3 years ago - 1 dependent repositories - 145 downloads last month - 0 stars on GitHub - 1 maintainer
geneparse 0.8.2
A suite of parse for genotype formats.
17 versions - Latest release: about 1 year ago - 3 dependent repositories - 214 downloads last month - 4 stars on GitHub - 1 maintainer
genetest 0.6.0
A package to process and analyze genotypic and phenotypic data.
8 versions - Latest release: over 2 years ago - 1 dependent repositories - 92 downloads last month - 3 stars on GitHub - 1 maintainer
sbsgenerator 1.0.5
Blazingly fast SBS matrix generator library
7 versions - Latest release: 3 months ago - 1.81 thousand downloads last month - 0 stars on GitHub - 1 maintainer
tidy-vcf 0.1.2.6
Make tidy VCF data.
4 versions - Latest release: 3 months ago - 1 dependent repositories - 36 downloads last month - 3 stars on GitHub - 1 maintainer
pybgen 0.7.1
Python module to read BGEN files.
11 versions - Latest release: over 3 years ago - 1 dependent package - 4 dependent repositories - 225 downloads last month - 5 stars on GitHub - 1 maintainer
Top 2.1% on pypi.org
msprime 1.3.1
Simulate genealogical trees and genomic sequence data using population genetic models
58 versions - Latest release: 4 months ago - 16 dependent packages - 83 dependent repositories - 5.33 thousand downloads last month - 167 stars on GitHub - 2 maintainers
Top 2.4% on pypi.org
hail 0.2.130
Scalable library for exploring and analyzing genomic data.
150 versions - Latest release: about 2 months ago - 10 dependent packages - 43 dependent repositories - 40.5 thousand downloads last month - 925 stars on GitHub - 2 maintainers
gennet-forked 2.0.0
Framework for Interpretable Neural Networks
2 versions - Latest release: 27 days ago - 1 dependent package - 227 downloads last month - 84 stars on GitHub - 1 maintainer
Top 9.9% on pypi.org
elucidatacmappy 3.3.4
Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute...
1 version - Latest release: over 1 year ago - 1 dependent package - 681 downloads last month - 117 stars on GitHub - 1 maintainer
Top 8.8% on pypi.org
cmappy 4.0.1
Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute...
36 versions - Latest release: over 5 years ago - 2 dependent packages - 1 dependent repositories - 1.82 thousand downloads last month - 117 stars on GitHub - 2 maintainers
cai 1.0.3
Python implementation of codon adaptation index
7 versions - Latest release: over 5 years ago - 1 dependent repositories - 176 downloads last month - 26 stars on GitHub - 1 maintainer
jupyter-locuszoom 0.1.1.dev0 💰
Jupyter Widget for LocusZoom
2 versions - Latest release: 11 months ago - 23 downloads last month - 4 stars on GitHub - 1 maintainer
brioche-enrichment 0.1.2a0
Bayesian tests for set enrichment.
1 version - Latest release: 11 months ago - 20 downloads last month - 1 stars on GitHub - 1 maintainer
gpubs 6
Pipeline to download and annotate gene-related publications
6 versions - Latest release: 10 months ago - 15 downloads last month - 1 maintainer
openoligo 0.1.7
An open-source platform for programmatically interacting with and managing Nucleic acid sequences...
8 versions - Latest release: 11 months ago - 54 downloads last month - 1 stars on GitHub - 1 maintainer
chromax 0.0.4a0
Breeding simulator based on JAX
4 versions - Latest release: 3 months ago - 1 dependent repositories - 40 downloads last month - 8 stars on GitHub - 1 maintainer
riboswitchinator 0.0.2
Tool to generate riboswitches for specific sequences
2 versions - Latest release: over 1 year ago - 6 downloads last month - 0 stars on GitHub - 1 maintainer
nimagen 0.0.3
Simple statistical and visualisation tool for neuroimaging genetics studies
3 versions - Latest release: about 1 year ago - 26 downloads last month - 0 stars on GitHub - 1 maintainer
vcf-kit 0.2.9
Assorted utilities for the variant call format
16 versions - Latest release: over 3 years ago - 1 dependent repositories - 202 downloads last month - 117 stars on GitHub - 1 maintainer
sisrs 0.1.0
Site Identification from Short Read Sequences.
1 version - Latest release: about 6 years ago - 1 dependent repositories - 13 downloads last month - 0 stars on GitHub - 1 maintainer
pytoxo 1.2
A Python tool to calculate penetrance tables for high-order epistasis models
3 versions - Latest release: about 2 years ago - 1 dependent repositories - 32 downloads last month - 2 stars on GitHub - 1 maintainer
pyplink 1.3.7
Python module to read binary Plink files.
13 versions - Latest release: 4 months ago - 2 dependent packages - 5 dependent repositories - 507 downloads last month - 14 stars on GitHub - 1 maintainer
pygenomics 0.1.5
A modern genomics library
4 versions - Latest release: about 7 years ago - 3 dependent repositories - 24 downloads last month - 17 stars on GitHub - 2 maintainers
pygenclean 1.8.3
Automated data clean up pipeline for genetic data
6 versions - Latest release: about 7 years ago - 1 dependent repositories - 49 downloads last month - 3 stars on GitHub - 1 maintainer
proofreader-polymerase 0.1.0
DNA proofreading
1 version - Latest release: over 2 years ago - 1 dependent repositories - 12 downloads last month - 1 stars on GitHub - 1 maintainer
picus 0.0.5
Pointed Interpretation of Clinical Variant Significance
5 versions - Latest release: over 3 years ago - 1 dependent repositories - 32 downloads last month - 0 stars on GitHub - 1 maintainer
Top 4.8% on pypi.org
pandas-plink 2.2.9
Read PLINK files into Pandas data frames
56 versions - Latest release: almost 3 years ago - 7 dependent packages - 22 dependent repositories - 5.87 thousand downloads last month - 75 stars on GitHub - 1 maintainer
mop-bam 0.0.6
Get well-mapped regions from bams
13 versions - Latest release: almost 3 years ago - 1 dependent repositories - 103 downloads last month - 19 stars on GitHub - 1 maintainer
mitopipeline 1.1.post8
Mitochondrial Genome Pipeline
16 versions - Latest release: almost 5 years ago - 1 dependent repositories - 81 downloads last month - 4 stars on GitHub - 1 maintainer
limix-plot 0.1.2
Plotting library for genetics.
14 versions - Latest release: about 5 years ago - 1 dependent repositories - 107 downloads last month - 1 stars on GitHub - 1 maintainer