Find open-source science resources
A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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10 of 9,815 resources
A library for high-throughput analyses of internal voids in biomolecules and ligand transport through them.
An ImageJ/FIJI macro to identify, count, and measure synaptic puncta from fluorescent images.
Workflow to perform aggregate rare variant tests for sequencing studies and genetic data. Implements the variant-Set Test for Association using Annotation infoRmation (STAAR) procedure, as well as SKAT, Burden, and ACAT tests for both continuous and dichotomous traits. The STAAR method incorporates qualitative functional categories and quantitative complementary functional annotations (Li and Li et al, 2020). The workflow accounts for population structure and relatedness, and scales for large whole genome sequencing studies.
Detect epistasis between SNPs along the edges of a gene-gene interaction network.
LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes.
A user-friendly tool for cloud-based whole slide image segmentation. Histo-cloud (HistomicsTK-deeplab) is a modified version of HistomicsTK by Brendon Lutnick. HistomicsTK is a Python package for the analysis of digital pathology images. It can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI.
A genome assembly correction and scaffolding pipeline using long reads.
A species-level analysis of 16S rRNA nanopore sequencing data based on de novo clustering and consensus building.
JAVA framework for accurate Variant assessment (JACUSA2) is a one-stop solution to detect single nucleotide variants (SNVs) and reverse transcriptase induced arrest events in Next-generation sequencing (NGS) data.
CHIMERA_AA is an integrated toolkit that allows researchers to modify and analyze protein structures and their complexes. This toolkit enables users to perform user-specified single or multiple amino acid mutations, as well as class-wise mutations, generating diverse structural combinations for further computational studies and generating initial coordinates of the mutated structures in user-specified formats (PDB, mmCIF, and mol2). The toolkit also generates minimized structures and facilitates the extraction and analysis of structural and physicochemical features of protein structures.