Open-source alternatives to Scanpy

Ceres Solver is a C++ library for numerical optimization, specializing in non-linear least squares and unconstrained optimization problems. It serves as a framework for automatic differentiation and robust curve fitting, providing tools to solve large-scale mathematical models. The library is distinguished by its bundle adjustment capabilities, which exploit sparse matrix structures to refine 3D scene points and camera parameters. It utilizes dual-number automatic differentiation to compute derivatives of cost functions, removing the need for manual Jacobian derivation. The project covers a

Memgraph is an in-memory, distributed graph database designed for high-performance labeled property graph management. It utilizes a Cypher query engine for declarative data retrieval and manipulation, providing a scalable knowledge graph backend that integrates vector search and graph traversals. The system distinguishes itself as a real-time graph analytics platform, employing native C++ and CUDA implementations to execute complex network analysis and dynamic community detection on streaming data. It provides specialized support for AI integration, including GraphRAG capabilities, the constr

Biopython is a bioinformatics library for Python providing tools to parse, manipulate, and analyze biological sequences, molecular structures, and phylogenetic trees. It serves as a biological sequence parser for genomic and proteomic data across multiple industry-standard file formats and acts as an interface for querying biological data and citations from NCBI Entrez repositories. The project distinguishes itself through specialized toolkits for protein structure analysis and phylogenetic tree construction. It includes a protein structure analyzer for processing PDB and mmCIF files to calcu

an htmlwidget for phylocanvas JS

Based on gosling.js and powered by shiny.react.

Based on Mol* (/'molstar/) and powered by shiny.react

🔬A library of JavaScript components to represent biological data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

HTML5 canvas genomic graphics library

:exclamation: This is a read-only mirror of the CRAN R package repository. chromoMap — Interactive Genomic Visualization of Biological Data

Flexible circular visualization of genome-associated data with BioPerl and SVG.

R/qtlcharts is an R package to create interactive charts for QTL data, for use with R/qtl.

📈 DNA Sequence Visualization for Humans

Shiny modules for visualizing flow cytometry data as well as data transformation methods to enable the rapid display of cytometry data. flowDashboard uses data objects that are derived from GatingSets to enable rapid deployment of comparative dashboards for large experiments. It is designed to…

SVG based genome viewer written in javascript using D3

Simple htmlwidgets binding R commands to the BioCircos.js library

TnT is a R package that wraps the TnT javascript libraries to provide track-based visulizations from R. It is useful for displaying genomic features as a simple genome browser, particularly when working with relevant Bioconductor packages.

:mountfuji: Fuji plot—a circos representation of multiple GWAS results— :mountfuji:

NGLVieweR - Visualize and interact with Protein Data Bank (PDB) and structural files in R and Shiny

Alexander Rose's nglviewer as an R/Shiny widget

The {safetyCharts} R package contains a set of charts used in clinical trial research. These charts are optimized for usage with the {safetyGraphics} package and shiny application, but can also easily be used as standalone displays.

An R htmlwidgets package of phylotree.js by @spond and @stevenweaver

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

msaR is a an htmlwidgets wrapper of the BioJS MSA viewer javascript library. msa will pass alignments to the BioJS MSA.

Interactive web-based genome browser.

3D Visualization of Brain MRI