DirichletMultinomial - Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.
Last updated
immunooncologymicrobiomesequencingclusteringclassificationmetagenomicsgsl
10.94 score 12 stars 27 dependents 154 scripts 9.3k downloadsAlphaMissenseR - Accessing AlphaMissense Data Resources in R
The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.
Last updated
snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology
7.19 score 13 stars 15 scripts 374 downloadscellxgenedp - Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.
Last updated
singlecelldataimportthirdpartyclient
6.70 score 9 stars 46 scripts 401 downloadsrjsoncons - Query, Pivot, Patch, and Validate 'JSON' and 'NDJSON'
Functions to query (filter or transform), pivot (convert from array-of-objects to object-of-arrays, for easy import as 'R' data frame), search, patch (edit), and validate (against 'JSON Schema') 'JSON' and 'NDJSON' strings, files, or URLs. Query and pivot support 'JSONpointer', 'JSONpath' or 'JMESpath' expressions. The implementation uses the 'jsoncons' <https://danielaparker.github.io/jsoncons/> header-only library; the library is easily linked to other packages for direct access to 'C++' functionality not implemented here.
Last updated
cpp
6.36 score 8 stars 14 dependents 9 scripts 1.4k downloads