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py-vobject
vobject

A full-featured Python package for parsing and creating iCalendar and vCard files

1.2M 52 14
brentp
cyvcf2

cython + htslib == fast VCF and BCF processing

208K 440 76
hail-is
hail

Cloud-native genomic dataframes and batch computing

88K 1K 264
bihealth
vcfpy

Python 3 library with good support for both reading and writing VCF

39K 112 24
apriha
snps

tools for reading, writing, generating, merging, and remapping SNPs

8K 115 18
sbslee
fuc

Frequently used commands in bioinformatics

7K 58 8
helicalAI
helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

7K 211 37
ACEnglish
truvari

Structural variant toolkit for VCFs

3K 407 60
TRON-Bioinformatics
vafator

Annotate variants in a VCF file with technical annotations from one or more BAMs

3K 10 0
aehrc
variant-spark

machine learning for genomic variants

1K 147 48
aprilweilab
igdtools

Tools for converting VCF to IGD files and processing them.

1K 21 0
vembrane
vembrane

Filter VCF/BCF files with Python expressions.

1K 69 5
dbmi-bgm
granite-suite

A collection of software to work with genomic variants

1K 7 0
varfish-org
mehari

Python bindings for the mehari variant annotator

1K 27 1
bihealth
varfish-cli

Command line interface client for VarFish Server.

1K 2 2
labsquare
cutevariant

A standalone and free application to explore genetics variations from VCF file

1K 108 21
KalinNonchev
gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

804 52 12
bigbio
pypgatk

Python tools for proteogenomics analysis toolkit

796 15 13
pwwang
vcfstats

Powerful statistics for VCF files

790 73 15
pieetie
svforge

🛠️ Reproducible, traceable synthetic SV VCFs for testing what your pipeline does to them. Caller-shaped Manta and DELLY outputs, real gnomAD/ENCODE injection with self-verifying tags. Synthetic data only.

703 1 0
robertopreste
hmtnote

Human mitochondrial variants annotation using HmtVar.

693 18 1
hail-is
j11hail

Scalable library for exploring and analyzing genomic data.

610 1K 264
remytuyeras
haplodynamics

A python library to develop genomic data simulators

526 4 0
EUCANCan
variant-extractor

Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.

454 7 1
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