The Top 23 Genomics Open Source Projects

Open source projects categorized as Genomics

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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

Seurat ⭐ 2,025

R toolkit for single cell genomics

dependent packages 2total releases 16most recent commit 3 months ago

Deeplearning Biology ⭐ 1,846

A list of deep learning implementations in biology

most recent commit a year ago

Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

dependent packages 32total releases 27most recent commit 3 months ago

Gatk ⭐ 1,576

Official code repository for GATK versions 4 and up

dependent packages 2total releases 46most recent commit a month ago

Bwa ⭐ 1,282

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

total releases 1most recent commit a year 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

Deep Review ⭐ 1,186

A collaboratively written review paper on deep learning, genomics, and precision medicine

most recent commit 2 years ago

Vg ⭐ 1,022

tools for working with genome variation graphs

most recent commit 3 months ago

Getting Started With Genomics Tools And Resources ⭐ 991

Unix, R and python tools for genomics and data science

most 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

Applied Computational Genomics ⭐ 887

Applied Computational Genomics Course at UU: Spring 2020

most 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

Nucleus ⭐ 675

Python and C++ code for reading and writing genomics data.

dependent packages 2total releases 18most recent commit 3 years 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

Bwa Mem2 ⭐ 645

The next version of bwa-mem

most 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

Igv.js ⭐ 608

Embeddable genomic visualization component based on the Integrative Genomics Viewer

dependent packages 11total releases 110most recent commit 3 months ago

The 10 Most Depended On 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

Htsjdk ⭐ 271

A Java API for high-throughput sequencing data (HTS) formats.

dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago

Cyvcf2 ⭐ 345

cython + htslib == fast VCF and BCF processing

dependent packages 46total releases 90latest release December 11, 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

Higlass ⭐ 300

Fast, flexible and extensible genome browser.

dependent packages 43total releases 240latest release November 28, 2023most recent commit 2 months ago

Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

dependent packages 32total releases 27latest release December 26, 2021most recent commit 3 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

Vcfr ⭐ 225

Tools to work with variant call format files

dependent packages 29total releases 16latest release December 08, 2023most recent commit 4 months ago

The 10 Latest Releases In Genomics Open Source Projects

Cyvcf2 ⭐ 345

cython + htslib == fast VCF and BCF processing

dependent packages 46total releases 90latest release December 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

Vcfr ⭐ 225

Tools to work with variant call format files

dependent packages 29total releases 16latest release December 08, 2023most recent commit 4 months ago

Gosling.js ⭐ 152

Grammar of Scalable Linked Interactive Nucleotide Graphics

dependent packages 5total releases 75latest release December 04, 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

Biomartr ⭐ 198

Genomic Data Retrieval with R

dependent packages 3total releases 21latest release December 02, 2023most recent commit 5 months ago

Fwdpy11 ⭐ 25

Forward-time simulation in Python using fwdpp

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

Alphasimr ⭐ 36

R package for breeding program simulations

dependent packages 3total releases 22latest release December 01, 2023most recent commit 3 months ago

Jbrowse Components ⭐ 182

Source code for JBrowse 2, a modern React-based genome browser

dependent packages 26total releases 79latest release November 30, 2023most recent commit 21 days ago

Higlass ⭐ 300

Fast, flexible and extensible genome browser.

dependent packages 43total releases 240latest release November 28, 2023most recent commit 2 months ago

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