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BASiCS

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

Bayesian Analysis of Single-Cell Sequencing data

Bioconductor version: Development (3.18)

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.

Author: Catalina Vallejos [aut, cre] , Nils Eling [aut], Alan O'Callaghan [aut], Sylvia Richardson [ctb], John Marioni [ctb]

Maintainer: Catalina Vallejos <catalina.vallejos at igmm.ed.ac.uk>

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

Installation

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

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

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

BiocManager::install("BASiCS")

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("BASiCS")
Introduction to BASiCS HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 2.13.4
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-3
Depends R (>= 4.2), SingleCellExperiment
Imports Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin
Linking To Rcpp, RcppArmadillo
Suggests BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick
System Requirements C++11
Enhances
URL https://github.com/catavallejos/BASiCS
Bug Reports https://github.com/catavallejos/BASiCS/issues
See More
Depends On Me BASiCStan
Imports Me
Suggests Me splatter
Links To Me
Build Report  

Package Archives

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

Source Package BASiCS_2.13.4.tar.gz
Windows Binary BASiCS_2.13.4.zip (64-bit only)
macOS Binary (x86_64) BASiCS_2.13.4.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/BASiCS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BASiCS
Bioc Package Browser https://code.bioconductor.org/browse/BASiCS/
Package Short Url https://bioconductor.org/packages/BASiCS/
Package Downloads Report Download Stats