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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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An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.
An R-based automated gating pipeline for flow cytometry data designed to mimic the manual gating strategy of defining flow biomarker positive populations relative to a unimodal background population to include cells with varying intensities of marker expression. The pipeline’s main feature is a flexible density-based gating strategy capable of capturing varying scenarios based on marker expression patterns to analyze a 29-marker flow panel that characterizes T-cell lineage, differentiation, and functional states.