BASiCS

DOI: 10.18129/B9.bioc.BASiCS    

Bayesian Analysis of Single-Cell Sequencing data

Bioconductor version: Release (3.6)

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 are quantified via a biological over-dispersion parameter that measures residual over-dispersion (with respect to Poisson sampling) after normalisation and technical noise removal.

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

Maintainer: Catalina A. Vallejos <cnvallej at uc.cl>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BASiCS")

Documentation

HTML	R Script	Introduction to BASiCS
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, CellBiology, DifferentialExpression, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.0.1
License	GPL (>= 2)
Depends	R (>= 3.4), SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.11.3), methods, coda, scran, testthat, data.table, matrixStats, graphics, KernSmooth, grDevices, stats, utils
LinkingTo	Rcpp, RcppArmadillo
Suggests	knitr, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/catavallejos/BASiCS
BugReports	https://github.com/catavallejos/BASiCS/issues
Depends On Me
Imports Me
Suggests Me	splatter
Build Report

Package Archives

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

Source Package	BASiCS_1.0.1.tar.gz
Windows Binary	BASiCS_1.0.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	BASiCS_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BASiCS
Package Short Url	http://bioconductor.org/packages/BASiCS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive