pagoda.view.aspects

Combined pathways that show similar expression patterns. Output of <code><a href="/link/pagoda.reduce.redundancy?package=scde&version=2.0.1" rd-options="" data-mini-rdoc="scde::pagoda.reduce.redundancy">pagoda.reduce.redundancy</a></code>

tamr

Dendrogram of combined pathways clustering

row.clustering

Restrict output to the top n aspects of heterogeneity

additional arguments are passed to the <code><a href="/link/view.aspects?package=scde&version=2.0.1" rd-options="" data-mini-rdoc="scde::view.aspects">view.aspects</a></code> method during plotting

Create static image of PAGODA output visualizing cell hierarchy and top aspects of transcriptional heterogeneity

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).

Peter Kharchenko

scde

Single Cell Differential Expression

pagoda.view.aspects function

Combined pathways that show similar expression patterns. Output of <code><a href="pagoda.reduce.redundancy" rd-options="">pagoda.reduce.redundancy</a></code>

additional arguments are passed to the <code><a href="view.aspects" rd-options="">view.aspects</a></code> method during plotting

pagoda.view.aspects: View PAGODA output

Description

Usage

Arguments

Value

Examples