DOI: 10.18129/B9.bioc.speckle  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see speckle.

Statistical methods for analysing single cell RNA-seq data

Bioconductor version: 3.17

The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.

Author: Belinda Phipson [aut, cre]

Maintainer: Belinda Phipson <phipson.b at wehi.edu.au>

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biocViews GeneExpression, RNASeq, Regression, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.2.0)
Imports limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics
Suggests BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0)
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