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Bioinformatics & Genomics Tools

Tools and libraries for analyzing biological data, particularly for genomics and single cell transcriptomics.

37 projects

24,009 contributors

$357M

Seurat

R toolkit for single cell genomics

Contributors

6,769

Organizations

306

Software value

$1.5M

Biopython

Biopython is an open-source library of tools for biological computation written in Python. It provides modules for working with biological sequences, file parsers for various bioinformatics file formats, access to online biological databases, and tools for performing common bioinformatics operations.

Contributors

2,080

Organizations

381

Software value

$62M

Scanpy

Single-cell analysis in Python. Scales to >1M cells.

Contributors

1,596

Organizations

216

Software value

$1.9M

BCFtools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Contributors

1,549

Organizations

195

Software value

$3.2M

SPAdes

SPAdes Genome Assembler

Contributors

1,372

Organizations

115

Software value

$49M

SAMtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

Contributors

1,200

Organizations

204

Software value

$1.7M

Integrative Genomics Viewer (IGV)

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Contributors

1,021

Organizations

157

Software value

$7.6M

cBioPortal

cBioPortal is an open-source platform for interactive exploration of cancer genomics datasets. It provides visualization, analysis, and download of large-scale cancer genomics data sets, integrating molecular profiles with clinical attributes and statistical analysis capabilities.

Contributors

949

Organizations

116

Software value

$7M

OpenMS

The codebase of the OpenMS project

Contributors

924

Organizations

105

Software value

$56M

MMseqs2

MMseqs2 (Many-against-Many sequence searching) is a high-performance software suite for protein sequence searching and clustering. It enables ultra-fast sequence searches and profile searches through sequence prefiltering, reduced amino acid alphabets, and parallelized processing, making it significantly faster than traditional tools while maintaining high sensitivity.

Contributors

897

Organizations

120

Software value

$15M

CellProfiler

An open-source application for biological image analysis

Contributors

738

Organizations

141

Software value

$6.3M

vg

tools for working with genome variation graphs

Contributors

720

Organizations

101

Software value

$8.8M

anvi'o

An analysis and visualization platform for 'omics data

Contributors

686

Organizations

60

Software value

$7.2M

anndata

Annotated data.

Contributors

564

Organizations

148

Software value

$901K

Nextstrain NCOV

Nextstrain build for SARS-CoV-2

Contributors

410

Organizations

64

Software value

$1.7M

WiGiTS

Various algorithms for analysing genomics data

Contributors

315

Organizations

28

Software value

$16M

PlantCV

Plant phenotyping with image analysis

Contributors

311

Organizations

18

Software value

$1.1M

BEAST X

Bayesian Evolutionary Analysis Sampling Trees

Contributors

269

Organizations

28

Software value

$33M

VSEARCH

Versatile open-source tool for microbiome analysis

Contributors

268

Organizations

64

Software value

$1.1M

Auspice

Web app for visualizing pathogen evolution

Contributors

266

Organizations

52

Software value

$1.5M

Cell Ontology

An ontology of cell types

Contributors

251

Organizations

41

Software value

$1.1M

Breedbase/SGN

The code behind the Sol Genomics Network, Cassavabase and other Breedbase websites

Contributors

242

Organizations

18

Software value

$47M

Nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Contributors

219

Organizations

38

Software value

$5.5M

Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

Contributors

204

Organizations

52

Software value

$1.6M

Tripal

Tripal is an open-source toolkit for constructing online biological/genomic databases. It provides a web interface and API for managing and displaying biological data by integrating with the Drupal content management system and Chado database schema.

Contributors

117

Organizations

20

Software value

$16M

Omics Playground

Visual self-service analytics platform for big omics data.

Contributors

72

Organizations

9

Software value

$3.4M

BioPerl

Core BioPerl 1.x code

This project hasn't been onboarded to LFX Insights.

Bioconda

Utilities for building and managing bioconda recipes

This project hasn't been onboarded to LFX Insights.

COBRA Toolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

This project hasn't been onboarded to LFX Insights.

Cactus

Official home of genome aligner based upon notion of Cactus graphs

This project hasn't been onboarded to LFX Insights.

Cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

This project hasn't been onboarded to LFX Insights.

Galaxy Tools Project

:microscope::books: Galaxy Tool wrappers

This project hasn't been onboarded to LFX Insights.

Pango Designation

Repository for suggesting new lineages that should be added to the current scheme

This project hasn't been onboarded to LFX Insights.

SeqAn

SeqAn's official repository.

This project hasn't been onboarded to LFX Insights.

SeqAn3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

This project hasn't been onboarded to LFX Insights.

Single-cell RNA-seq Pipeline

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

This project hasn't been onboarded to LFX Insights.
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