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speckle

This is the development version of speckle; for the stable release version, see speckle.

Statistical methods for analysing single cell RNA-seq data


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("speckle")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("speckle")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("speckle")
speckle: statistical methods for analysing single cell RNA-seq data HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, RNASeq, Regression, SingleCell, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package speckle_1.3.0.tar.gz
Windows Binary speckle_1.3.0.zip
macOS Binary (x86_64) speckle_1.3.0.tgz
macOS Binary (arm64) speckle_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/speckle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/speckle
Bioc Package Browser https://code.bioconductor.org/browse/speckle/
Package Short Url https://bioconductor.org/packages/speckle/
Package Downloads Report Download Stats