scde: Single Cell Differential Expression

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The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).

Author
Peter Kharchenko [aut, cre], Jean Fan [aut]
Date of publication
None
Maintainer
Jean Fan <jeanfan@fas.harvard.edu>
License
GPL-2
Version
2.2.0
URLs

View on Bioconductor

Man pages

bwpca
Determine principal components of a matrix using...
clean.counts
Filter counts matrix
clean.gos
Filter GOs list
es.mef.small
Sample data
knn
Sample error model
knn.error.models
Build error models for heterogeneous cell populations, based...
make.pagoda.app
Make the PAGODA app
o.ifm
Sample error model
pagoda.cluster.cells
Determine optimal cell clustering based on the genes driving...
pagoda.effective.cells
Estimate effective number of cells based on lambda1 of random...
pagoda.gene.clusters
Determine de-novo gene clusters and associated overdispersion...
pagoda.pathway.wPCA
Run weighted PCA analysis on pre-annotated gene sets
pagoda.reduce.loading.redundancy
Collapse aspects driven by the same combinations of genes
pagoda.reduce.redundancy
Collapse aspects driven by similar patterns (i.e. separate...
pagoda.show.pathways
View pathway or gene weighted PCA
pagoda.subtract.aspect
Control for a particular aspect of expression heterogeneity...
pagoda.top.aspects
Score statistical significance of gene set and cluster...
pagoda.varnorm
Normalize gene expression variance relative to...
pagoda.view.aspects
View PAGODA output
papply
wrapper around different mclapply mechanisms
pollen
Sample data
scde
Single-cell Differential Expression (with Pathway And Gene...
scde.browse.diffexp
View differential expression results in a browser
scde.edff
Internal model data
scde.error.models
Fit single-cell error/regression models
scde.expression.difference
Test for expression differences between two sets of cells
scde.expression.magnitude
Return scaled expression magnitude estimates
scde.expression.prior
Estimate prior distribution for gene expression magnitudes
scde.failure.probability
Calculate drop-out probabilities given a set of counts or...
scde.fit.models.to.reference
Fit scde models relative to provided set of expression...
scde.posteriors
Calculate joint expression magnitude posteriors across a set...
scde.test.gene.expression.difference
Test differential expression and plot posteriors for a...
show.app
View PAGODA application
view.aspects
View heatmap
ViewPagodaApp-class
A Reference Class to represent the PAGODA application
winsorize.matrix
Winsorize matrix

Files in this package

scde/DESCRIPTION
scde/NAMESPACE
scde/R
scde/R/functions.R
scde/data
scde/data/es.mef.small.rda
scde/data/knn.rda
scde/data/o.ifm.rda
scde/data/pollen.rda
scde/data/scde.edff.rda
scde/man
scde/man/ViewPagodaApp-class.Rd
scde/man/bwpca.Rd
scde/man/clean.counts.Rd
scde/man/clean.gos.Rd
scde/man/es.mef.small.Rd
scde/man/knn.Rd
scde/man/knn.error.models.Rd
scde/man/make.pagoda.app.Rd
scde/man/o.ifm.Rd
scde/man/pagoda.cluster.cells.Rd
scde/man/pagoda.effective.cells.Rd
scde/man/pagoda.gene.clusters.Rd
scde/man/pagoda.pathway.wPCA.Rd
scde/man/pagoda.reduce.loading.redundancy.Rd
scde/man/pagoda.reduce.redundancy.Rd
scde/man/pagoda.show.pathways.Rd
scde/man/pagoda.subtract.aspect.Rd
scde/man/pagoda.top.aspects.Rd
scde/man/pagoda.varnorm.Rd
scde/man/pagoda.view.aspects.Rd
scde/man/papply.Rd
scde/man/pollen.Rd
scde/man/scde.Rd
scde/man/scde.browse.diffexp.Rd
scde/man/scde.edff.Rd
scde/man/scde.error.models.Rd
scde/man/scde.expression.difference.Rd
scde/man/scde.expression.magnitude.Rd
scde/man/scde.expression.prior.Rd
scde/man/scde.failure.probability.Rd
scde/man/scde.fit.models.to.reference.Rd
scde/man/scde.posteriors.Rd
scde/man/scde.test.gene.expression.difference.Rd
scde/man/show.app.Rd
scde/man/view.aspects.Rd
scde/man/winsorize.matrix.Rd
scde/src
scde/src/Makevars
scde/src/Makevars.win
scde/src/bwpca.cpp
scde/src/bwpca.h
scde/src/jpmatLogBoot.cpp
scde/src/jpmatLogBoot.h
scde/src/matSlideMult.cpp
scde/src/matSlideMult.h
scde/src/pagoda.cpp
scde/src/pagoda.h
scde/vignettes
scde/vignettes/diffexp.Rmd
scde/vignettes/pagoda.Rmd