R-universe - genecell (Min Dai)

COSG - Marker Gene Identification for Single Cell Sequencing Data

COSG is designed for accurate and ultra-fast marker gene identification in single-cell sequencing data. COSG can not only be applied to single-cell RNA-seq data, but also single-cell ATAC-seq data and spatial transcriptomics.

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marker-genespiasoscatac-seqscrna-seqspatial-transcriptomics

5.16 score 67 stars 144 scripts

cytome - Native R Reader and Streaming Interface for the Cytome Single-Cell Store

Reads .cytome files - a SQLite-backed single-cell store - natively in R with zero Python dependency. A .cytome is a plain SQLite database, so the structural data (cells / genes / peaks, embeddings, graphs, fragments) is read with DBI; the chunked, compressed CSR count matrices are decoded via a small Rcpp layer (lz4-block / zstd / zlib). Constructs a SingleCellExperiment or a Seurat object, and provides cytome-native chunk streaming for out-of-core analysis without loading the full matrix. Part of the PIASO toolkit for single-cell omics (<https://piaso.org>).

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piasolz4libzstdzlibcpp

2.18 score 1 stars 5 scripts