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

Top 8.1% on pypi.org
pycirclize 1.5.0
Circular visualization in Python
20 versions - Latest release: 5 days ago - 7 dependent packages - 1 dependent repositories - 2.39 thousand downloads last month - 629 stars on GitHub - 1 maintainer
genomehubs 2.8.8
GenomeHubs
152 versions - Latest release: 6 days ago - 1 dependent repositories - 1.27 thousand downloads last month - 13 stars on GitHub - 1 maintainer
dajin2 0.4.6
One-step genotyping tools for targeted long-read sequencing
46 versions - Latest release: 6 days ago - 406 downloads last month - 4 stars on GitHub - 1 maintainer
flatgfa 0.1.3
efficient processing of pangenomes in Graphical Fragment Assembly (GFA) format
2 versions - Latest release: 7 days ago - 415 downloads last month - 24 stars on GitHub - 1 maintainer
nmdc-schema 10.3.0
Schema resources for the National Microbiome Data Collaborative (NMDC)
74 versions - Latest release: 7 days ago - 1.66 thousand downloads last month - 26 stars on GitHub - 4 maintainers
pytantan 0.1.1
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and ...
2 versions - Latest release: 8 days ago - 2.5 thousand downloads last month - 0 stars on GitHub - 1 maintainer
blasttools 0.1.16
Commands for turning blast queries into pandas dataframes.
6 versions - Latest release: 9 days ago - 1.63 thousand downloads last month - 0 stars on GitHub - 1 maintainer
Top 9.0% on pypi.org
hicstuff 3.2.3
General purpose stuff to generate and handle Hi-C data in its simplest form.
130 versions - Latest release: 9 days ago - 1 dependent package - 4 dependent repositories - 1.89 thousand downloads last month - 35 stars on GitHub - 5 maintainers
genomicsdb 0.0.9.13
Experimental Python Bindings for querying GenomicsDB
18 versions - Latest release: 9 days ago - 1 dependent repositories - 1.06 thousand downloads last month - 1 stars on GitHub - 3 maintainers
pyranges1 1.0.1
GenomicRanges for Python.
6 versions - Latest release: 11 days ago - 1 dependent package - 610 downloads last month - 5 stars on GitHub - 2 maintainers
greatbrowser 0.0.1
Automate Stanford's GREAT browser
6 versions - Latest release: 11 days ago - 1.44 thousand downloads last month - 0 stars on GitHub - 1 maintainer
wgd 2.0.38
wgd
28 versions - Latest release: 11 days ago - 609 downloads last month - 17 stars on GitHub - 1 maintainer
Top 5.1% on pypi.org
jcvi 1.4.12
Python utility libraries on genome assembly, annotation and comparative genomics
110 versions - Latest release: 12 days ago - 1 dependent package - 3 dependent repositories - 1.75 thousand downloads last month - 702 stars on GitHub - 1 maintainer
geneweaver-db 0.3.8
Database Interaction Services for GeneWeaver
46 versions - Latest release: 13 days ago - 1.66 thousand downloads last month - 4 stars on GitHub - 1 maintainer
Top 2.7% on pypi.org
pyranges 0.1.1
GenomicRanges for Python.
120 versions - Latest release: 13 days ago - 56 dependent packages - 56 dependent repositories - 15.5 thousand downloads last month - 389 stars on GitHub - 2 maintainers
Top 9.0% on pypi.org
gencove 2.16.3
Gencove API and CLI tool
120 versions - Latest release: 13 days ago - 1 dependent repositories - 22 thousand downloads last month - 3 stars on GitHub - 1 maintainer
readfish 2024.2.0
ONT adaptive sampling
10 versions - Latest release: 14 days ago - 1 dependent repositories - 285 downloads last month - 161 stars on GitHub - 3 maintainers
odm-sdk 1.57.0
SDK for interacting with the Open Data Manager
2 versions - Latest release: 14 days ago - 8 downloads last month - 3 stars on GitHub - 1 maintainer
pyopal 0.6.0
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
16 versions - Latest release: 14 days ago - 1 dependent package - 1 dependent repositories - 4.16 thousand downloads last month - 7 stars on GitHub - 1 maintainer
galaxy-tool-shed 24.0.2
Galaxy auth framework and implementations
4 versions - Latest release: 16 days ago - 102 downloads last month - 1,315 stars on GitHub - 1 maintainer
galaxy-test-driver 24.0.2
Galaxy test driver
18 versions - Latest release: 16 days ago - 1 dependent package - 1 dependent repositories - 185 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-web-apps 24.0.2
Galaxy web apps
15 versions - Latest release: 16 days ago - 2 dependent packages - 1 dependent repositories - 233 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.4% on pypi.org
galaxy-app 24.0.2
Galaxy application (backend)
19 versions - Latest release: 16 days ago - 4 dependent packages - 13 dependent repositories - 450 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.1% on pypi.org
galaxy-web-stack 24.0.2
Galaxy web stack abstraction
18 versions - Latest release: 16 days ago - 5 dependent packages - 10 dependent repositories - 437 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.1% on pypi.org
galaxy-web-framework 24.0.2
Galaxy web framework
19 versions - Latest release: 16 days ago - 4 dependent packages - 10 dependent repositories - 423 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-test-api 24.0.2
Galaxy API tests
18 versions - Latest release: 16 days ago - 1 dependent repositories - 186 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.1% on pypi.org
galaxy-job-execution 24.0.2
Galaxy job execution runtime utilities
20 versions - Latest release: 16 days ago - 5 dependent packages - 10 dependent repositories - 430 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.2% on pypi.org
galaxy-auth 24.0.2
Galaxy auth framework and implementations
19 versions - Latest release: 16 days ago - 2 dependent packages - 10 dependent repositories - 396 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.1% on pypi.org
galaxy-test-base 24.0.2
Galaxy testing utilities
18 versions - Latest release: 16 days ago - 2 dependent packages - 9 dependent repositories - 272 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-tours 24.0.2
Galaxy tours backend framework
15 versions - Latest release: 16 days ago - 1 dependent package - 362 downloads last month - 1,315 stars on GitHub - 1 maintainer
galaxy-selenium 24.0.2
Galaxy Selenium interaction framework
19 versions - Latest release: 16 days ago - 1 dependent repositories - 222 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.9% on pypi.org
galaxy-data 24.0.2
Galaxy datatype framework and datatypes
24 versions - Latest release: 16 days ago - 9 dependent packages - 13 dependent repositories - 782 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 1.6% on pypi.org
galaxy-tool-util 24.0.2
Galaxy tool and tool dependency utilities
60 versions - Latest release: 16 days ago - 16 dependent packages - 43 dependent repositories - 19.6 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-schema 24.0.2
Galaxy auth framework and implementations
4 versions - Latest release: 16 days ago - 111 downloads last month - 1,315 stars on GitHub - 1 maintainer
Top 3.6% on pypi.org
galaxy-objectstore 24.0.2
Galaxy objectstore framework and plugins
25 versions - Latest release: 16 days ago - 5 dependent packages - 13 dependent repositories - 824 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-navigation 24.0.2
Galaxy client DOM navigation framework
15 versions - Latest release: 16 days ago - 2 dependent packages - 417 downloads last month - 1,315 stars on GitHub - 1 maintainer
Top 3.8% on pypi.org
galaxy-job-metrics 24.0.2
Galaxy job metrics
22 versions - Latest release: 16 days ago - 3 dependent packages - 10 dependent repositories - 665 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.4% on pypi.org
galaxy-files 24.0.2
Galaxy file source framework and default plugins
16 versions - Latest release: 16 days ago - 4 dependent packages - 6 dependent repositories - 499 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.1% on pypi.org
galaxy-config 24.0.2
Galaxy configuration
16 versions - Latest release: 16 days ago - 3 dependent packages - 3 dependent repositories - 393 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 1.9% on pypi.org
galaxy-util 24.0.2
Galaxy generic utilities
36 versions - Latest release: 16 days ago - 23 dependent packages - 23 dependent repositories - 19.8 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.9% on pypi.org
cogent3 2024.5.7a1
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems ...
21 versions - Latest release: 16 days ago - 5 dependent packages - 5 dependent repositories - 1.72 thousand downloads last month - 95 stars on GitHub - 1 maintainer
pyfamsa 0.4.0
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence ali...
8 versions - Latest release: 17 days ago - 3 dependent packages - 2.44 thousand downloads last month - 21 stars on GitHub - 1 maintainer
mustache-hic 1.3.3
Mustache is a Hi-C analysis tool
49 versions - Latest release: 18 days ago - 1 dependent repositories - 437 downloads last month - 53 stars on GitHub - 4 maintainers
phykit 1.19.4
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
65 versions - Latest release: 19 days ago - 1 dependent repositories - 1.06 thousand downloads last month - 46 stars on GitHub - 1 maintainer
Top 8.9% on pypi.org
seqlogo 5.29.9
Python port of the R Bioconductor `seqlogo` package
38 versions - Latest release: 20 days ago - 2 dependent packages - 3 dependent repositories - 495 downloads last month - 25 stars on GitHub - 1 maintainer
sphae 1.3.3
Assembling pure culture phages from both Illumina and Nanopore sequencing technology
7 versions - Latest release: 20 days ago - 313 downloads last month - 17 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: 22 days ago - 5 dependent packages - 13 dependent repositories - 2.39 thousand downloads last month - 16 stars on GitHub - 1 maintainer
Top 8.2% on pypi.org
fastlmm 0.6.8
Fast GWAS
52 versions - Latest release: 22 days ago - 1 dependent package - 7 dependent repositories - 680 downloads last month - 43 stars on GitHub - 4 maintainers
geonomics 1.4.1
A package for landscape genomic simulation
69 versions - Latest release: 23 days ago - 7 dependent repositories - 509 downloads last month - 9 stars on GitHub - 1 maintainer
ahab-lib 1.0.1
Python CLI library for interacting with ahab cloud API and Kubernetes systems.
1 version - Latest release: 23 days ago - 148 downloads last month - 0 stars on GitHub - 1 maintainer
clipkit 2.3.0
Alignment trimming software for phylogenetics.
44 versions - Latest release: 23 days ago - 1 dependent repositories - 728 downloads last month - 52 stars on GitHub - 1 maintainer
seqpro 0.1.12
Elucidating the Utility of Genomic Elements with Neural Nets
12 versions - Latest release: 26 days ago - 3 dependent packages - 83 downloads last month - 59 stars on GitHub - 2 maintainers
Top 5.9% on pypi.org
bed-reader 1.0.4
Read and write the PLINK BED format, simply and efficiently.
33 versions - Latest release: 27 days ago - 7 dependent packages - 4 dependent repositories - 22 thousand downloads last month - 67 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: 29 days ago - 3 dependent packages - 4 dependent repositories - 322 downloads last month - 87 stars on GitHub - 2 maintainers
Top 5.3% on pypi.org
cooltools 0.7.0
Analysis tools for genomic interaction data stored in .cool format
14 versions - Latest release: about 1 month ago - 3 dependent packages - 7 dependent repositories - 520 downloads last month - 120 stars on GitHub - 3 maintainers
geneweaver-core 0.9.1
The core of the Jax-Geneweaver Python library
47 versions - Latest release: about 1 month ago - 4 dependent packages - 1 dependent repositories - 772 downloads last month - 4 stars on GitHub - 1 maintainer
checkqc 4.0.2
A simple program to parse Illumina NGS data and check it for quality criteria.
37 versions - Latest release: about 1 month ago - 1 dependent repositories - 658 downloads last month - 24 stars on GitHub - 3 maintainers
Top 9.6% on pypi.org
gnomad 0.8.0
Hail utilities for the Genome Aggregation Database
13 versions - Latest release: about 1 month ago - 1 dependent repositories - 2.48 thousand downloads last month - 82 stars on GitHub - 2 maintainers
chewbbaca 3.3.5
A complete suite for gene-by-gene schema creation and strain identification.
40 versions - Latest release: about 1 month ago - 1 dependent repositories - 398 downloads last month - 118 stars on GitHub - 5 maintainers
Top 5.1% on pypi.org
pybbi 0.4.0
Python bindings to the UCSC source for Big Binary Indexed (bigWig/bigBed) files.
14 versions - Latest release: about 1 month ago - 2 dependent packages - 9 dependent repositories - 1.83 thousand downloads last month - 26 stars on GitHub - 1 maintainer
Top 2.4% on pypi.org
goatools 1.4.4
Python scripts to find enrichment of GO terms
50 versions - Latest release: about 1 month ago - 18 dependent packages - 51 dependent repositories - 6.32 thousand downloads last month - 727 stars on GitHub - 1 maintainer
omicidx 1.11.3
The OmicIDX project collects, reprocesses, and then republishes metadata from multiple public gen...
54 versions - Latest release: about 1 month ago - 1 dependent repositories - 603 downloads last month - 12 stars on GitHub - 1 maintainer
fgpyo 0.3.0 💰
Python bioinformatics and genomics library
14 versions - Latest release: about 1 month ago - 1 dependent package - 1 dependent repositories - 877 downloads last month - 23 stars on GitHub - 3 maintainers
hiscanner 0.2a0
High-resolution copy number variant calling in single-cell whole-genome sequencing.
2 versions - Latest release: about 1 month ago - 1 dependent package - 87 downloads last month - 0 stars on GitHub - 1 maintainer
Top 2.4% on pypi.org
hail 0.2.130
Scalable library for exploring and analyzing genomic data.
150 versions - Latest release: about 1 month ago - 10 dependent packages - 43 dependent repositories - 40.5 thousand downloads last month - 925 stars on GitHub - 2 maintainers
crunchstat_summary 2.7.2
Arvados crunchstat-summary reads crunch log files and summarizes resource usage
20 versions - Latest release: about 1 month ago - 92 downloads last month - 365 stars on GitHub - 1 maintainer
arvados_fuse 2.7.2
Arvados FUSE driver
503 versions - Latest release: about 1 month ago - 2 dependent repositories - 1.28 thousand downloads last month - 365 stars on GitHub - 1 maintainer
Top 9.9% on pypi.org
arvados-cwl-runner 2.7.2
Arvados Common Workflow Language runner
361 versions - Latest release: about 1 month ago - 5 dependent repositories - 1.56 thousand downloads last month - 365 stars on GitHub - 1 maintainer
Top 5.5% on pypi.org
arvados-python-client 2.7.2
Arvados client library
689 versions - Latest release: about 1 month ago - 11 dependent repositories - 6.93 thousand downloads last month - 365 stars on GitHub - 1 maintainer
fwdpy11 0.22.2
Forward-time population genetic simulation in Python
106 versions - Latest release: about 1 month ago - 1 dependent repositories - 2.45 thousand downloads last month - 27 stars on GitHub - 1 maintainer
allcools 1.1.0
Toolkit for single-cell DNA methylome and multiomic data analysis.
41 versions - Latest release: about 1 month ago - 1 dependent repositories - 324 downloads last month - 33 stars on GitHub - 1 maintainer
mopepgen 1.4.0
Multi-omic peptide generator
1 version - Latest release: about 1 month ago - 164 downloads last month - 5 stars on GitHub - 1 maintainer
genomkit 0.2.8
genomkit
6 versions - Latest release: about 1 month ago - 45 downloads last month - 0 stars on GitHub - 1 maintainer
cancer_data 0.3.6
Preprocessing for various cancer genomics datasets
13 versions - Latest release: about 2 months ago - 211 downloads last month - 14 stars on GitHub - 1 maintainer
Top 3.8% on pypi.org
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
cgat 0.7.2
cgat : the Computational Genomics Analysis Toolkit
35 versions - Latest release: about 2 months ago - 202 downloads last month - 3 maintainers
bycon 1.6.5
A Python-based environment for the Beacon v2 genomics API
76 versions - Latest release: about 2 months ago - 339 downloads last month - 4 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 2 months ago - 2 dependent packages - 8 dependent repositories - 1.73 thousand downloads last month - 31 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 2 months ago - 110 downloads last month - 29 stars on GitHub - 1 maintainer
Top 8.5% on pypi.org
truvari 4.2.2
Structural variant comparison tool for VCFs
26 versions - Latest release: about 2 months ago - 2 dependent repositories - 605 downloads last month - 295 stars on GitHub - 1 maintainer
soda-gallery 1.2.0
Python-based UCSC genome browser gallery generator
3 versions - Latest release: about 2 months ago - 1 dependent repositories - 75 downloads last month - 12 stars on GitHub - 1 maintainer
Top 2.1% on pypi.org
mappy 2.28
Minimap2 python binding
29 versions - Latest release: about 2 months ago - 27 dependent packages - 49 dependent repositories - 5.16 thousand downloads last month - 1,698 stars on GitHub - 1 maintainer
gnomonicus 2.5.3
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
29 versions - Latest release: about 2 months ago - 1 dependent repositories - 162 downloads last month - 5 stars on GitHub - 1 maintainer
dysgu 1.6.3
Structural variant calling
28 versions - Latest release: about 2 months ago - 1 dependent repositories - 954 downloads last month - 85 stars on GitHub - 1 maintainer
pandasgwas 1.2.2
A Python package for easy retrieval of GWAS Catalog data
17 versions - Latest release: about 2 months ago - 118 downloads last month - 6 stars on GitHub - 1 maintainer
phables 1.3.2
Phables: from fragmented assemblies to high-quality bacteriophage genomes
21 versions - Latest release: 2 months ago - 1 dependent repositories - 72 downloads last month - 62 stars on GitHub - 1 maintainer
geneweaver-testing 0.1.2
A library to standardize testing of GeneWeaver pacakges.
22 versions - Latest release: 2 months ago - 1 dependent repositories - 604 downloads last month - 4 stars on GitHub - 1 maintainer
Top 4.8% on pypi.org
sevenbridges-python 2.11.0
SBG API python client bindings
122 versions - Latest release: 2 months ago - 3 dependent packages - 15 dependent repositories - 82.6 thousand downloads last month - 45 stars on GitHub - 1 maintainer
superpang 1.3.0
Non-redundant pangenome assemblies from multiple genomes or bins
18 versions - Latest release: 2 months ago - 1 dependent repositories - 25 downloads last month - 11 stars on GitHub - 1 maintainer
pegasuspy 1.9.1
Pegasus is a Python package for analyzing sc/snRNA-seq data of millions of cells
42 versions - Latest release: 2 months ago - 1 dependent repositories - 1.17 thousand downloads last month - 69 stars on GitHub - 3 maintainers
neosv 0.0.4
Neoantigens from Structural Variations
3 versions - Latest release: 2 months ago - 52 downloads last month - 1 maintainer
sbsgenerator 1.0.5
Blazingly fast SBS matrix generator library
7 versions - Latest release: 2 months ago - 1.81 thousand downloads last month - 0 stars on GitHub - 1 maintainer
bioflow-insight 0.0.31
A software to extract and analyze the structure and associated metadata from a Nextflow workflow.
23 versions - Latest release: 2 months ago - 86 downloads last month - 63 stars on GitHub - 1 maintainer
prfect 0.41
A tool to predict programmed ribosomal frameshifts
19 versions - Latest release: 2 months ago - 1 dependent repositories - 243 downloads last month - 7 stars on GitHub - 1 maintainer
pybarrnap 0.5.0
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
7 versions - Latest release: 2 months ago - 55 downloads last month - 7 stars on GitHub - 1 maintainer
cellxgene-gateway 0.4.0
Cellxgene Gateway
19 versions - Latest release: 2 months ago - 1 dependent repositories - 333 downloads last month - 52 stars on GitHub - 1 maintainer
Top 3.4% on pypi.org
deeptools 3.5.5
Useful tools for exploring deep sequencing data.
60 versions - Latest release: 3 months ago - 6 dependent packages - 36 dependent repositories - 2.33 thousand downloads last month - 645 stars on GitHub - 3 maintainers
rnalib 0.0.3
A python-based transcriptomics library
3 versions - Latest release: 3 months ago - 36 downloads last month - 1 stars on GitHub - 1 maintainer
ipr 3.13.0
Python adapter for generating reports uploaded to IPR using the PORI platform
28 versions - Latest release: 3 months ago - 1 dependent repositories - 198 downloads last month - 6 stars on GitHub - 2 maintainers
cptac 1.5.13
Python packaging for CPTAC data
59 versions - Latest release: 3 months ago - 1 dependent repositories - 673 downloads last month - 79 stars on GitHub - 2 maintainers
Related Keywords
bioinformatics 351 python 100 sequencing 64 ngs 45 dna 39 genetics 38 pipeline 37 workflow 37 science 35 workflow-engine 32 visualization 31 biology 29 hacktoberfest 27 usegalaxy 26 Galaxy 21 alignment 19 deep-learning 19 machine-learning 19 metagenomics 18 hi-c 17 genome 16 evolution 15 bioinformatics-pipeline 15 sequence 14 rna-seq 14 genomics-visualization 14 single-cell 14 phylogenetics 14 vcf 14 cancer 13 gwas 13 computational-biology 12 protein 12 deep learning 12 next-generation-sequencing 11 variant 11 mapping 11 computational biology 11 microbial-genomics 11 bacteria 11 transcriptomics 11 comparative-genomics 11 variants 10 poa 10 microbial 10 rna 10 cuda 10 python-api 10 analysis 10 sequence-alignment 10 partial-order-alignment 10 gpu 10 nvidia 10 computational 10 proteomics 10 epigenomics 9 research 9 assembly 9 data 8 pathogen 8 infectious-diseases 8 global-health 8 cloud 8 genome-analysis 8 variation 8 motif 8 genomic-data-analysis 8 machine learning 8 microbiology 8 fasta 7 artificial intelligence 7 python-library 7 development 7 python3 7 data-science 7 bioinformatics-tool 7 aws 7 docker 7 cancer-genomics 7 variant-calling 7 phylogenomics 7 genomes 7 structural-variation 7 genotype 6 epigenetics 6 metadata 6 sequence-analysis 6 azure 6 phylogeny 6 long-reads 6 phage 6 genbank 6 biopython 6 bigdata 6 population-genetics 6 gtf 6 gcp 6 pandas 6 Hi-C 6 model zoo 6