speckle

Statistical methods for analysing single cell RNA-seq data

Bioconductor version: Release (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>

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

Installation

To install this package, start R (version "4.3") and enter:

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

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	1.0.0
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
Linking To
Suggests	BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0)
System Requirements
Enhances
URL

Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	speckle_1.0.0.tar.gz
Windows Binary	speckle_1.0.0.zip
macOS Binary (x86_64)	speckle_1.0.0.tgz
macOS Binary (arm64)	speckle_1.0.0.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