BASiCS_Data-methods

show,BASiCS_Data-method

counts

counts,BASiCS_Data-method

displaySpikeInput

displaySpikeInput,BASiCS_Data-method

displayTechIndicator

displayTechIndicator,BASiCS_Data-method

displayGeneNames

displayGeneNames,BASiCS_Data-method

displayBatchInfo

displayBatchInfo,BASiCS_Data-method

A <code>BASiCS_Data</code> object.

object

Only required for <code>counts</code> method. A string indicating which genes are returned.

type

S4 methods for <code><a rd-options="BASiCS" href="/link/BASiCS_Data-class?package=BASiCS&version=0.7.30&to=BASiCS" data-mini-rdoc="BASiCS::BASiCS_Data-class">BASiCS_Data-class</a></code> objects.

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 unexplained 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 where: (ii)
cell-specific normalization constants are estimated as part of the model
parameters, (ii) technical variability is quantified based on spike-in
genes that are artificially introduced to each analysed cells lysate and
(iii) the total variability of the expression counts is decomposed into
technical and biological components. BASiCS also provides an intuitive
detection criterion for highly (or lowly) variable genes within the
population of cells under study. This is formalized by means of tail
posterior probabilities associated to high (or low) biological cell-to-cell
variance contributions, quantities that can be easily interpreted by
applied users. Additionally, BASiCS has now been extended to compare gene
expression patterns between pre-specified populations 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 the removal of technical variation.

Catalina Vallejos

BASiCS

Bayesian Analysis of Single-Cell Sequencing data

BASiCS_Data-methods function

S4 methods for <code><a rd-options='BASiCS' href='BASiCS_Data-class'>BASiCS_Data-class</a></code> objects.

S4 methods for BASiCS_Data objects — BASiCS_Data-methods

S4 methods for BASiCS_Data objects

BASiCS_Data-methods: S4 methods for BASiCS_Data objects

Description

Usage

Arguments

Value

References

See Also

Examples