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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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dinoR tests for significant differences in NOMe-seq footprints between two conditions, using genomic regions of interest (ROI) centered around a landmark, for example a transcription factor (TF) motif. This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input. dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin), plot the percentage of fragments in each category in a heatmap, or averaged across different ROI groups, for example, containing a common TF motif. It is designed to compare footprints between two sample groups, using edgeR's quasi-likelihood methods on the total fragment counts per ROI, sample, and footprint category.