speckle
Statistical methods for analysing single cell RNA-seq data
Bioconductor version: Release (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("speckle")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, RNASeq, Regression, SingleCell, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | speckle_1.4.0.tar.gz |
| Windows Binary (x86_64) | speckle_1.4.0.zip |
| macOS Binary (x86_64) | speckle_1.4.0.tgz |
| macOS Binary (arm64) | speckle_1.4.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |