The Top 23 Python Genomics Open Source Projects

Open source projects categorized as Python Genomics

Categories > Science > Genomics

Categories > Programming Languages > Python

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

dependent packages 1,373total releases 58most recent commit 3 months ago

Deepvariant ⭐ 2,978

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

most recent commit 4 months ago

Pymatgen ⭐ 1,254

Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.

dependent packages 225total releases 370most recent commit 3 months ago

Galaxy ⭐ 1,211

Data intensive science for everyone.

dependent packages 23total releases 30most recent commit 3 months ago

Adam ⭐ 966

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

dependent packages 17total releases 14most recent commit 3 months ago

Hail ⭐ 905

Cloud-native genomic dataframes and batch computing

dependent packages 17total releases 146most recent commit 3 months ago

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

dependent packages 6total releases 25most recent commit 9 months ago

Goatools ⭐ 673

Python library to handle Gene Ontology (GO) terms

dependent packages 30total releases 47most recent commit 5 months ago

Jcvi ⭐ 650

Python library to facilitate genome assembly, annotation, and comparative genomics

dependent packages 1total releases 97most recent commit 4 months ago

Deeptools ⭐ 644

Tools to process and analyze deep sequencing data.

most recent commit 11 days ago

Seq ⭐ 624

A high-performance, Pythonic language for bioinformatics

most recent commit a year ago

Orthofinder ⭐ 547

Phylogenetic orthology inference for comparative genomics

most recent commit a year ago

Pycirclize ⭐ 476

Circular visualization in Python (Circos Plot, Chord Diagram)

dependent packages 3total releases 13most recent commit 4 months ago

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

dependent packages 119total releases 86most recent commit 3 months ago

Pyranges ⭐ 371

Performant Pythonic GenomicRanges

dependent packages 46total releases 117most recent commit 4 months ago

Enformer Pytorch ⭐ 359

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

dependent packages 1total releases 98most recent commit 4 months ago

Arvados ⭐ 354

An open source platform for managing and analyzing biomedical big data

total releases 9most recent commit 3 months ago

Nucleotide Transformer ⭐ 305

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

most recent commit 3 months ago

Canvasxpress ⭐ 282

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

dependent packages 4total releases 43most recent commit 3 months ago

Genometools ⭐ 261

GenomeTools genome analysis system.

most recent commit 5 months ago

Pygeno ⭐ 242

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

total releases 18most recent commit 4 years ago

Intermine ⭐ 228

A powerful open source data warehouse system

dependent packages 2total releases 8most recent commit 2 years ago

Hgvs ⭐ 226

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

dependent packages 12total releases 104most recent commit 3 months ago

The 10 Most Depended On Python Genomics Open Source Projects

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

dependent packages 1,373total releases 58latest release February 13, 2023most recent commit 3 months ago

Pymatgen ⭐ 1,254

dependent packages 225total releases 370latest release November 13, 2023most recent commit 3 months ago

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

dependent packages 119total releases 86latest release September 22, 2023most recent commit 3 months ago

Pyranges ⭐ 371

Performant Pythonic GenomicRanges

dependent packages 46total releases 117latest release June 29, 2023most recent commit 4 months ago

Goatools ⭐ 673

Python library to handle Gene Ontology (GO) terms

dependent packages 30total releases 47latest release November 04, 2023most recent commit 5 months ago

Cooler ⭐ 183

A cool place to store your Hi-C

dependent packages 27total releases 45latest release September 11, 2023most recent commit 3 months ago

Galaxy ⭐ 1,211

Data intensive science for everyone.

dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months ago

Tskit ⭐ 131

Population-scale genomics

dependent packages 17total releases 36latest release October 10, 2023most recent commit 3 months ago

Adam ⭐ 966

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

dependent packages 17total releases 14latest release December 16, 2020most recent commit 3 months ago

Hail ⭐ 905

Cloud-native genomic dataframes and batch computing

dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months ago

The 10 Latest Releases In Python Genomics Open Source Projects

Galaxy ⭐ 1,211

Data intensive science for everyone.

dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months ago

Algebra ⭐ 10

A Boolean Algebra for Genetic Variants

dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months ago

Fwdpy11 ⭐ 25

Forward-time simulation in Python using fwdpp

total releases 103latest release December 01, 2023most recent commit 3 months ago

Scarf ⭐ 83

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

dependent packages 1total releases 43latest release November 24, 2023most recent commit 3 months ago

Gecco ⭐ 45

GEne Cluster prediction with COnditional random fields.

total releases 29latest release November 23, 2023most recent commit 5 months ago

Pybio ⭐ 7

pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs.

dependent packages 2total releases 27latest release November 23, 2023most recent commit 4 months ago

Glue Genes ⭐ 7

glue for genomics and transcriptomics

total releases 7latest release November 22, 2023most recent commit 4 months ago

Biocommons.seqrepo ⭐ 34

non-redundant, compressed, journalled, file-based storage for biological sequences

dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months ago

Pymatgen ⭐ 1,254

dependent packages 225total releases 370latest release November 13, 2023most recent commit 3 months ago

Biokit ⭐ 20

a versatile toolkit for processing and analyzing diverse types of sequence data

total releases 13latest release November 11, 2023most recent commit 4 months ago

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