Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

Nature Methods
Jean FanPeter V Kharchenko

Abstract

The transcriptional state of a cell reflects a variety of biological factors, from cell-type-specific features to transient processes such as the cell cycle, all of which may be of interest. However, identifying such aspects from noisy single-cell RNA-seq data remains challenging. We developed pathway and gene set overdispersion analysis (PAGODA) to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

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Datasets Mentioned

BETA
GSE60361
GSE59739
GSE76005

Methods Mentioned

BETA
scRNA-seq
PCA
Smart-Seq
RNA-seq
fluorescence activated single cell sorting
GAM

Software Mentioned

GP
SRA
Bowtie2
Samtools
Tophat
hclust
PAGODA
Seq
brainmapr
GSEA

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