Ecosyste.ms: Packages

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

pypi.org "genomics" keyword

fings 1.7.1
Filters for Next Generation Sequencing
4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 46 downloads last month - 8 stars on GitHub - 2 maintainers
cellograph 0.0.6
cellograph
6 versions - Latest release: about 1 year ago - 60 downloads last month - 3 stars on GitHub - 2 maintainers
python-outbreak-info 1.0.4
Python interface to Outbreak.info, powered by GISAID
3 versions - Latest release: 3 months ago - 1 dependent repositories - 117 downloads last month - 6 stars on GitHub - 2 maintainers
python-outbreak-data 1.0 removed
Python interface to Outbreak.info, powered by GISAID
1 version - Latest release: about 1 year ago - 4 downloads last month - 5 stars on GitHub - 2 maintainers
clipkit 2.3.0
Alignment trimming software for phylogenetics.
44 versions - Latest release: 4 days ago - 1 dependent repositories - 736 downloads last month - 52 stars on GitHub - 1 maintainer
mixs-linkml 0.1.3
A LinkML model for the MIxS standard
3 versions - Latest release: almost 2 years ago - 1 dependent repositories - 29 downloads last month - 33 stars on GitHub - 4 maintainers
uorf4u 0.9.5
A tool for short uORF annotation.
42 versions - Latest release: almost 1 year ago - 90 downloads last month - 10 stars on GitHub - 2 maintainers
orthofisher 1.1.0
orthofisher
20 versions - Latest release: 6 months ago - 1 dependent repositories - 187 downloads last month - 24 stars on GitHub - 2 maintainers
wormbase-parasite 0.5.0
An interface to the Wormbase REST API
3 versions - Latest release: about 3 years ago - 1 dependent repositories - 46 downloads last month - 3 stars on GitHub - 1 maintainer
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 - 10 maintainers
dnadiffusion 0.0.0.dev0
Library for probabilistic analysis of protein-protein interaction sequencing data.
1 version - Latest release: about 1 year ago - 18 downloads last month - 335 stars on GitHub - 1 maintainer
Top 2.5% on pypi.org
tskit 0.5.6
The tree sequence toolkit.
36 versions - Latest release: 7 months ago - 12 dependent packages - 54 dependent repositories - 10.9 thousand downloads last month - 143 stars on GitHub - 2 maintainers
cgp-dss-data-loader 1.1.0
Simple data loader for CGP HCA Data Store
4 versions - Latest release: over 5 years ago - 64 downloads last month - 2 stars on GitHub - 2 maintainers
flowcraft 1.4.1
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
18 versions - Latest release: about 5 years ago - 1 dependent repositories - 148 downloads last month - 238 stars on GitHub - 2 maintainers
gmql 0.1.1
Python Library for data analysis based on GMQL
13 versions - Latest release: almost 5 years ago - 1 dependent repositories - 85 downloads last month - 11 stars on GitHub - 1 maintainer
pyfamsa 0.3.2
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence ali...
7 versions - Latest release: 3 months ago - 1.59 thousand downloads last month - 21 stars on GitHub - 2 maintainers
Top 7.0% on pypi.org
pairtools 1.1.0
CLI tools to process mapped Hi-C data
11 versions - Latest release: 10 days ago - 2 dependent packages - 4 dependent repositories - 322 downloads last month - 87 stars on GitHub - 2 maintainers
open-cravat-multiuser 2.5.0
OpenCRAVAT Multiuser Addon
10 versions - Latest release: 2 months ago - 1 dependent repositories - 57 downloads last month - 106 stars on GitHub - 2 maintainers
crisprbact 0.3.11
Tools to design and analyse CRISPRi experiments
15 versions - Latest release: about 4 years ago - 119 downloads last month - 2 maintainers
phykit 1.19.4
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
65 versions - Latest release: about 9 hours ago - 1 dependent repositories - 886 downloads last month - 46 stars on GitHub - 2 maintainers
boss_runs 0.1.0
Dynamic, adaptive sampling during nanopore sequencing
1 version - Latest release: about 2 months ago - 25 downloads last month - 160 stars on GitHub - 2 maintainers
readfish 2023.1.1
ONT adaptive sampling
8 versions - Latest release: 7 months ago - 1 dependent repositories - 146 downloads last month - 160 stars on GitHub - 6 maintainers
bw-merge-window 0.2.0
A python extension for quick access to bigWig and bigBed files.
2 versions - Latest release: 4 months ago - 23 downloads last month - 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
cosmos-wfm 2.13.11
Workflow Management System
229 versions - Latest release: over 3 years ago - 4 dependent repositories - 481 downloads last month - 70 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 13 hours ago - 2 dependent packages - 3 dependent repositories - 495 downloads last month - 25 stars on GitHub - 2 maintainers
ga4gh-client 0.0.5
A client for the GA4GH reference server
8 versions - Latest release: over 7 years ago - 3 dependent repositories - 95 downloads last month - 6 stars on GitHub - 4 maintainers
genomedashboard 0.0.90
Genome Dashboard is the logic behind a web-based prototype of a genomics dashboard, specifically ...
64 versions - Latest release: over 4 years ago - 1 dependent repositories - 411 downloads last month - 2 stars on GitHub - 4 maintainers
synthego-ice 1.2.0
Synthego - Inference of CRISPR Edits (ICE)
4 versions - Latest release: over 4 years ago - 1 dependent repositories - 44 downloads last month - 59 stars on GitHub - 1 maintainer
genomicassertions 0.2.5
A package to test common files in genomics (.vcf.gz, .bam)
3 versions - Latest release: almost 8 years ago - 3 dependent repositories - 17 downloads last month - 1 maintainer
pyranges1 0.1.1
GenomicRanges for Python.
2 versions - Latest release: 3 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
Top 9.9% on pypi.org
cgatcore 0.6.16
cgatcore : the Computational Genomics Analysis Toolkit
32 versions - Latest release: about 1 month ago - 2 dependent packages - 8 dependent repositories - 1.73 thousand downloads last month - 31 stars on GitHub - 4 maintainers
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
seq-pigeon 0.4.3
Pipeline tool for NGS data
17 versions - Latest release: over 3 years ago - 1 dependent repositories - 89 downloads last month - 933 stars on GitHub - 2 maintainers
mdeepfri 1.1.5
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
5 versions - Latest release: about 1 month ago - 301 downloads last month - 27 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
pyclaragenomics-cuda-10-0 0.4.3
NVIDIA genomics python libraries and utiliites
2 versions - Latest release: over 4 years ago - 1 dependent repositories - 6 downloads last month - 275 stars on GitHub - 2 maintainers
geneweaver-testing 0.1.2
A library to standardize testing of GeneWeaver pacakges.
22 versions - Latest release: about 2 months ago - 1 dependent repositories - 604 downloads last month - 4 stars on GitHub - 1 maintainer
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
wgd 2.0.35
wgd
25 versions - Latest release: 3 days ago - 434 downloads last month - 14 stars on GitHub - 2 maintainers
pegasuspy 1.9.1
Pegasus is a Python package for analyzing sc/snRNA-seq data of millions of cells
42 versions - Latest release: about 2 months ago - 1 dependent repositories - 1.07 thousand downloads last month - 69 stars on GitHub - 6 maintainers
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
genomicsdb 0.0.9.11
Experimental Python Bindings for querying GenomicsDB
16 versions - Latest release: 16 days ago - 1 dependent repositories - 796 downloads last month - 1 stars on GitHub - 6 maintainers
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
nmdc_schema 10.2.0
Schema resources for the National Microbiome Data Collaborative (NMDC)
70 versions - Latest release: 15 days ago - 2.56 thousand downloads last month - 26 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
mdmcleaner 0.8.7
A pipeline for the assessment, classification and refinement of microbial dark matter SAGs and MAGs
5 versions - Latest release: over 1 year ago - 1 dependent repositories - 58 downloads last month - 18 stars on GitHub - 1 maintainer
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 - 190 downloads last month - 775 stars on GitHub - 3 maintainers
Top 9.9% on pypi.org
arvados-cwl-runner 2.7.2
Arvados Common Workflow Language runner
361 versions - Latest release: 24 days ago - 5 dependent repositories - 1.65 thousand downloads last month - 364 stars on GitHub - 1 maintainer
Top 5.5% on pypi.org
arvados-python-client 2.7.2
Arvados client library
689 versions - Latest release: 24 days ago - 11 dependent repositories - 6.32 thousand downloads last month - 363 stars on GitHub - 1 maintainer
arvados_fuse 2.7.2
Arvados FUSE driver
503 versions - Latest release: 24 days ago - 2 dependent repositories - 1.54 thousand downloads last month - 363 stars on GitHub - 1 maintainer
arvados-pam 2.0.4
Arvados PAM module
32 versions - Latest release: over 3 years ago - 99 downloads last month - 363 stars on GitHub - 1 maintainer
crunchstat_summary 2.7.2
Arvados crunchstat-summary reads crunch log files and summarizes resource usage
20 versions - Latest release: 24 days ago - 302 downloads last month - 363 stars on GitHub - 1 maintainer
mitty 2.29.0
Simulator for genomic data
4 versions - Latest release: over 5 years ago - 1 dependent repositories - 27 downloads last month - 13 stars on GitHub - 2 maintainers
Top 9.6% on pypi.org
genepattern-notebook 23.1.0
GenePattern Notebook extension for JupyterLab
64 versions - Latest release: about 1 year ago - 1 dependent package - 4 dependent repositories - 440 downloads last month - 44 stars on GitHub - 2 maintainers
fwdpy11 0.22.2
Forward-time population genetic simulation in Python
106 versions - Latest release: 24 days ago - 1 dependent repositories - 2.45 thousand downloads last month - 27 stars on GitHub - 1 maintainer
easyae 0.0.0
easy way for non-linear dimensionality increase or reduction
1 version - Latest release: about 5 years ago - 1 dependent repositories - 15 downloads last month - 0 stars on GitHub - 2 maintainers
geneweaver-db 0.3.4
Database Interaction Services for GeneWeaver
39 versions - Latest release: 1 day ago - 800 downloads last month - 4 stars on GitHub - 2 maintainers
superpang 1.3.0
Non-redundant pangenome assemblies from multiple genomes or bins
18 versions - Latest release: about 2 months ago - 1 dependent repositories - 25 downloads last month - 11 stars on GitHub - 2 maintainers
Top 0.6% on pypi.org
biopython 1.83
Freely available tools for computational molecular biology.
60 versions - Latest release: 4 months ago - 637 dependent packages - 3,405 dependent repositories - 829 thousand downloads last month - 3,908 stars on GitHub - 5 maintainers
mah51-biopython 1.1
Freely available tools for computational molecular biology.
2 versions - Latest release: almost 2 years ago - 1 dependent repositories - 28 downloads last month - 3,900 stars on GitHub - 1 maintainer
dajin2 0.4.5
One-step genotyping tools for targeted long-read sequencing
45 versions - Latest release: 10 days ago - 367 downloads last month - 4 stars on GitHub - 2 maintainers
candig-schemas 1.1.0
CanDIG API Schemas
4 versions - Latest release: almost 4 years ago - 2 dependent repositories - 58 downloads last month - 1 stars on GitHub - 4 maintainers
Top 8.8% on pypi.org
coolbox 0.3.8
Jupyter notebook based genomic data visulization toolkit.
20 versions - Latest release: almost 3 years ago - 1 dependent package - 2 dependent repositories - 109 downloads last month - 211 stars on GitHub - 2 maintainers
Top 9.0% on pypi.org
enformer-pytorch 0.8.8 💰
Enformer - Pytorch
99 versions - Latest release: 5 months ago - 1 dependent repositories - 902 downloads last month - 373 stars on GitHub - 1 maintainer
Top 7.9% on pypi.org
pyrle 0.0.40
Numeric run length encoding for Python.
40 versions - Latest release: 3 days ago - 2 dependent packages - 13 dependent repositories - 2.39 thousand downloads last month - 16 stars on GitHub - 1 maintainer
Top 2.4% on pypi.org
goatools 1.4.4
Python scripts to find enrichment of GO terms
48 versions - Latest release: 21 days ago - 17 dependent packages - 51 dependent repositories - 6.18 thousand downloads last month - 727 stars on GitHub - 1 maintainer
pyclaragenomics-cuda-10-1 0.4.3
NVIDIA genomics python libraries and utiliites
2 versions - Latest release: over 4 years ago - 1 dependent repositories - 12 downloads last month - 273 stars on GitHub - 2 maintainers
Top 7.3% on pypi.org
peddy 0.4.8 💰
pleasingly pythonic pedigree manipulation
27 versions - Latest release: almost 3 years ago - 7 dependent repositories - 1.69 thousand downloads last month - 127 stars on GitHub - 2 maintainers
Top 2.2% on pypi.org
cyvcf2 0.30.28 💰
fast vcf parsing with cython + htslib
93 versions - Latest release: 3 months ago - 33 dependent packages - 99 dependent repositories - 62.7 thousand downloads last month - 357 stars on GitHub - 1 maintainer
sradownload 2.6
downloads SRA short reads from either NCBI or EBI and converts them into fastq.gz files
14 versions - Latest release: almost 2 years ago - 1 dependent repositories - 49 downloads last month - 0 stars on GitHub - 2 maintainers
galaxy-navigation 24.0.1
Galaxy client DOM navigation framework
14 versions - Latest release: 1 day ago - 2 dependent packages - 417 downloads last month - 1,315 stars on GitHub - 2 maintainers
Top 3.8% on pypi.org
galaxy-job-metrics 24.0.1
Galaxy job metrics
21 versions - Latest release: 1 day ago - 3 dependent packages - 10 dependent repositories - 665 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.1% on pypi.org
galaxy-test-base 24.0.1
Galaxy testing utilities
17 versions - Latest release: 1 day ago - 2 dependent packages - 9 dependent repositories - 272 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.4% on pypi.org
galaxy-app 24.0.1
Galaxy application (backend)
18 versions - Latest release: 1 day ago - 4 dependent packages - 13 dependent repositories - 450 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.4% on pypi.org
galaxy-files 24.0.1
Galaxy file source framework and default plugins
15 versions - Latest release: 1 day ago - 4 dependent packages - 6 dependent repositories - 499 downloads last month - 1,315 stars on GitHub - 6 maintainers
Top 4.1% on pypi.org
galaxy-job-execution 24.0.1
Galaxy job execution runtime utilities
19 versions - Latest release: 1 day ago - 5 dependent packages - 10 dependent repositories - 421 downloads last month - 1,315 stars on GitHub - 6 maintainers
galaxy-schema 24.0.1
Galaxy auth framework and implementations
3 versions - Latest release: 1 day ago - 111 downloads last month - 1,315 stars on GitHub - 2 maintainers
galaxy-selenium 24.0.1
Galaxy Selenium interaction framework
18 versions - Latest release: 1 day ago - 1 dependent repositories - 217 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 3.6% on pypi.org
galaxy-objectstore 24.0.1
Galaxy objectstore framework and plugins
24 versions - Latest release: 1 day ago - 5 dependent packages - 13 dependent repositories - 824 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.1% on pypi.org
galaxy-web-framework 24.0.1
Galaxy web framework
18 versions - Latest release: 1 day ago - 4 dependent packages - 10 dependent repositories - 414 downloads last month - 1,315 stars on GitHub - 6 maintainers
Top 6.1% on pypi.org
galaxy-config 24.0.1
Galaxy configuration
15 versions - Latest release: 1 day ago - 3 dependent packages - 3 dependent repositories - 393 downloads last month - 1,315 stars on GitHub - 5 maintainers
Top 5.2% on pypi.org
galaxy-auth 24.0.1
Galaxy auth framework and implementations
18 versions - Latest release: 1 day ago - 2 dependent packages - 10 dependent repositories - 396 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-test-api 24.0.1
Galaxy API tests
17 versions - Latest release: 1 day ago - 1 dependent repositories - 172 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.9% on pypi.org
galaxy-data 24.0.1
Galaxy datatype framework and datatypes
23 versions - Latest release: 1 day ago - 8 dependent packages - 13 dependent repositories - 669 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-test-driver 24.0.1
Galaxy test driver
17 versions - Latest release: 1 day ago - 1 dependent package - 1 dependent repositories - 185 downloads last month - 1,315 stars on GitHub - 6 maintainers
galaxy-tool-shed 24.0.1
Galaxy auth framework and implementations
3 versions - Latest release: 1 day ago - 102 downloads last month - 1,315 stars on GitHub - 2 maintainers
Top 5.1% on pypi.org
galaxy-web-stack 24.0.1
Galaxy web stack abstraction
17 versions - Latest release: 1 day ago - 3 dependent packages - 10 dependent repositories - 370 downloads last month - 1,315 stars on GitHub - 6 maintainers
galaxy-tours 24.0.1
Galaxy tours backend framework
14 versions - Latest release: 1 day ago - 1 dependent package - 342 downloads last month - 1,315 stars on GitHub - 2 maintainers
galaxy-web-apps 24.0.1
Galaxy web apps
14 versions - Latest release: 1 day ago - 1 dependent package - 1 dependent repositories - 212 downloads last month - 1,315 stars on GitHub - 3 maintainers
ezclermont 0.7.0
ezclermont: phylotype your E. coli strains, in silico
10 versions - Latest release: over 2 years ago - 1 dependent repositories - 53 downloads last month - 9 stars on GitHub - 1 maintainer
Top 9.0% on pypi.org
concise 0.6.9
CONCISE (COnvolutional Neural for CIS-regulatory Elements)
25 versions - Latest release: about 4 years ago - 1 dependent package - 4 dependent repositories - 532 downloads last month - 32 stars on GitHub - 4 maintainers
deepbreaks 1.1.2
deepBreaks: a machine learning tool for identifying and prioritizing genotype-phenotype associations
5 versions - Latest release: 9 months ago - 63 downloads last month - 8 stars on GitHub - 2 maintainers
proms 1.0.12
Protein Markers Selection
10 versions - Latest release: about 1 year ago - 1 dependent repositories - 65 downloads last month - 6 stars on GitHub - 1 maintainer
microbecensus 1.2.2
A command-line tool for estimating average genome size from shotgun sequence data
8 versions - Latest release: 8 months ago - 1 dependent repositories - 43 downloads last month - 37 stars on GitHub - 1 maintainer
broad-genepy 1.2.6 💰
A useful module for any CompBio
11 versions - Latest release: over 1 year ago - 53 downloads last month - 18 stars on GitHub - 2 maintainers
pyfish 1.0.3
Plotting tool for evolutionary population dynamics. Creates a Fish (Muller) plot.
4 versions - Latest release: about 1 year ago - 1 dependent package - 1 dependent repositories - 40 downloads last month - 4 maintainers
cbio-py 0.1.4
This is a python client for the cBioPortal API
7 versions - Latest release: over 1 year ago - 206 downloads last month - 5 stars on GitHub - 2 maintainers
pybedlite 0.0.4 💰
Python classes for interfacing with bed intervals
2 versions - Latest release: 8 months ago - 1 dependent repositories - 641 downloads last month - 12 stars on GitHub - 2 maintainers
Related Keywords
bioinformatics 348 python 99 sequencing 65 ngs 45 dna 39 genetics 37 pipeline 37 workflow 37 science 35 workflow-engine 32 visualization 31 biology 29 hacktoberfest 27 usegalaxy 26 Galaxy 21 machine-learning 19 deep-learning 19 alignment 19 metagenomics 18 hi-c 17 genome 16 bioinformatics-pipeline 15 evolution 15 vcf 14 phylogenetics 14 genomics-visualization 14 single-cell 14 rna-seq 14 sequence 13 gwas 13 deep learning 12 protein 12 computational-biology 12 cancer 12 variant 11 bacteria 11 mapping 11 microbial-genomics 11 computational biology 11 comparative-genomics 11 next-generation-sequencing 11 transcriptomics 11 python-api 10 poa 10 variants 10 microbial 10 sequence-alignment 10 partial-order-alignment 10 nvidia 10 gpu 10 cuda 10 rna 10 proteomics 10 computational 10 epigenomics 9 research 9 assembly 9 analysis 9 global-health 8 machine learning 8 infectious-diseases 8 pathogen 8 genomic-data-analysis 8 genome-analysis 8 microbiology 8 variation 8 motif 8 cloud 8 data 8 python3 7 aws 7 docker 7 data-science 7 artificial intelligence 7 structural-variation 7 phylogenomics 7 development 7 variant-calling 7 fasta 7 cancer-genomics 7 genomes 7 bioinformatics-tool 7 pandas 6 genotype 6 oxford-nanopore 6 epigenetics 6 genbank 6 metadata 6 biopython 6 sequence-analysis 6 population-genetics 6 phage 6 reference 6 gcp 6 bigdata 6 azure 6 long-reads 6 galaxy 6 cooler 6 python-library 6