Find open-source science resources
Cross-domain directory aggregating tools, AI models, datasets, and research resources from bio.tools, Bioconductor, HuggingFace, curated GitHub awesome-lists, and more.
Filters
Domain
Language
License
Source
Type(1)
3,084 of 5,674 resources
Showing 2,901–2,950
A Library for Deep Learning in Biology and Chemistry.
DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.
Molecular property prediction with unified API for diverse models and respresentations,
ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
Vector representations of molecular substructures.
Descriptor computation(chemistry) and (optional) storage for machine learning.
Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).
Simple RDKit molecule editor GUI using PySide.
Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).
An object-oriented, webGL based JavaScript library for online molecular visualization.
A swiss army knife for manipulating and editing PDB files.
A script to run structural alerts using the RDKit and ChEMBL
Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).
Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
Toolkit for processing molecules, reactions and condensed graphs of reactions. Can be used for chemical standardization, MCS search, tautomers generation with backward compatibility to RDKit and NetworkX.
- Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.
Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
Resources on ChIP-seq data which include papers, methods, links to software, and analysis.
[@crazyhottommy](https://github.com/crazyhottommy)'s notes on various steps and considerations when doing RNA-seq analysis.
Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.
A collection of research papers for AI-based protein design.
List of resources on alternative splicing including software, databases, and other tools.
Solid path for those of you who want to complete a Bioinformatics course on your own time, for free, with courses from the best universities in the World.
A circos representation of multiple GWAS results.
Perl package for circular plots, which are well suited for genomic rearrangements.
JavaScript library for drawing canvas-based gene diagrams.
JavaScript library that can be used to generate interactive and highly customizable web-based genome browsers.
JavaScript genome browser that is highly customizable via plugins and track customizations.
D3 JavaScript based genome viewer. Constructs SVGs.
Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats.
Horizon chart D3-based JavaScript library for DNA data.
Flexible circular visualization of genome-associated data with BioPerl and SVG.
BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.
Embeddable genome viewer. Integration data from a wide variety of sources, and can load data directly from popular genomics file formats including bigWig, BAM, and VCF.
Easy-to-use DNA sequence visualization tool that turns FASTA files into browser-based visualizations.
A fuzzy Bruijn graph approach to long noisy reads assembly
A haplotype-resolved assembler for accurate Hifi reads.
De novo assembler for single molecule sequencing reads using repeat graphs.
A single molecule sequence assembler for genomes large and small.
Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.
Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.
Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.
SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.
Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.