Bioconductor classes, generics and methods, implemented in Javascript.
The Javascript (browser) end of websocket, 4-field JSON messaging, companion to R package BrowserViz
R-based utilities for proteinpaint
Single cell RNA-seq analysis in Javascript
A yeoman-generator for R projects
Retrieving parts of a SummarizedExperiment via HTTP range requests.
Pure-Rust port of the GSVA family of gene-set enrichment methods (GSVA, ssGSEA, z-score, PLAGE), validated for numeric parity against the Bioconductor GSVA package.
Pure-Rust port of the Bioconductor limma differential-expression package
Pure-Rust port of quanTIseq (Finotello et al. 2019) immune-cell deconvolution — constrained least squares against the TIL10 signature — validated for numeric parity against the Bioconductor quantiseqr package.
The original version of caching files is implemented in R as a part of Bioconductor project: https://www.bioconductor.org/packages/release/bioc/html/BiocFileCache.html
A rust implementation of GenomicDistributions package from bioconductor.
Rust CLI toolkit for niche optimized genomics file processing and target-based variant workflows
A Rust library and command line tool for genomic range operations.
Per-gene average log2-CPM of a count matrix via the edgeR aveLogCPM one-group negative-binomial fit
Counts-per-million (CPM) and log2-CPM normalization of a gene count matrix, edgeR-compatible
DESeq2 fpkm(): median-of-ratios robust-normalized FPKM of a gene count matrix given per-gene basepair lengths
DESeq2 fpm(): fragments per million of a gene count matrix, robust median-of-ratios library sizes (default) or raw column totals
DESeq2 normTransform: log2(count / size-factor + 1) of a gene count matrix