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.
Filters
Health
Domain(1)
Language
License(1)
Source(1)
Type
4 of 7,088 resources
Generates pre-miRNA and mature miRNA count tables from read alignments to pre-miRNA sequences and a gff file, both downloaded from mirBase. Produces also read coverage plots of pre-miRNAs.
jaxQTL is a flexible and efficient sc-eQTL mapping framework using count-based models, designed to analyze sparse counts in scRNA-seq data and large datasets. It has been shown to identify more eGenes compared with existing approaches, improving our ability to identify distal eQTLs.
Local Windows-friendly R Shiny application for RNA-seq differential expression using DESeq2, normalized-expression testing, over-representation analysis, fgsea-ranked pathway analysis, and WGCNA coexpression-network analysis. It supports input validation, additive and interaction designs, built-in human, fruit-fly, and yeast annotations, publication-quality plots, and reproducibility bundles containing results, settings, and executable R and R Markdown rerun code.
Tool to generate a count matrix for expression data in Galaxy. generate_count_matrix reads in one or more input text files with expression counts and produces a single combined file. Each input will have a column in the matrix containing expression values. The column containing gene (or feature) names should be identical for all input count files.