37 projects
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.