Man pages for hms-dbmi/scde
Single Cell Differential Expression

bwpcaDetermine principal components of a matrix using...
clean.countsFilter counts matrix
clean.gosFilter GOs list
es.mef.smallSample data
knnSample error model
knn.error.modelsBuild error models for heterogeneous cell populations, based...
make.pagoda.appMake the PAGODA app
o.ifmSample error model
pagoda.cluster.cellsDetermine optimal cell clustering based on the genes driving...
pagoda.effective.cellsEstimate effective number of cells based on lambda1 of random...
pagoda.gene.clustersDetermine de-novo gene clusters and associated overdispersion...
pagoda.pathway.wPCARun weighted PCA analysis on pre-annotated gene sets
pagoda.reduce.loading.redundancyCollapse aspects driven by the same combinations of genes
pagoda.reduce.redundancyCollapse aspects driven by similar patterns (i.e. separate...
pagoda.show.pathwaysView pathway or gene weighted PCA
pagoda.subtract.aspectControl for a particular aspect of expression heterogeneity...
pagoda.top.aspectsScore statistical significance of gene set and cluster...
pagoda.varnormNormalize gene expression variance relative to...
pagoda.view.aspectsView PAGODA output
papplywrapper around different mclapply mechanisms
pollenSample data
scdeSingle-cell Differential Expression (with Pathway And Gene...
scde.browse.diffexpView differential expression results in a browser
scde.error.modelsFit single-cell error/regression models
scde.expression.differenceTest for expression differences between two sets of cells
scde.expression.magnitudeReturn scaled expression magnitude estimates
scde.expression.priorEstimate prior distribution for gene expression magnitudes
scde.failure.probabilityCalculate drop-out probabilities given a set of counts or...
scde.fit.models.to.referenceFit scde models relative to provided set of expression...
scde.posteriorsCalculate joint expression magnitude posteriors across a set...
scde.test.gene.expression.differenceTest differential expression and plot posteriors for a...
show.appView PAGODA application
view.aspectsView heatmap
ViewPagodaApp-classA Reference Class to represent the PAGODA application
winsorize.matrixWinsorize matrix
hms-dbmi/scde documentation built on June 19, 2017, 10:31 p.m.