pcaReduce statistics

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pcaReduce specifications


Unique identifier OMICS_11385
Name pcaReduce
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
pcaMethods, mnormt, mclust
Maintained Yes


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  • person_outline Christopher Yau <>

Publication for pcaReduce

pcaReduce in publications

PMCID: 5737331
PMID: 28973464
DOI: 10.1093/nar/gkx681

[…] is based on principal component analysis (pca). pca has been used extensively for clustering single cells (,,). other groups have developed new methods which extend and improve pca. these include pcareduce (), which uses a novel agglomerative clustering method on top of pca to cluster the cells. snn-cliq () constructs a shared k-nearest neighbor (knn) graph over all the cells with the weight […]

PMCID: 5030210
PMID: 27708664
DOI: 10.3389/fgene.2016.00163

[…] ). for example, jaitin et al. combined hierarchical clustering and probabilistic mixture models to classify single cells from different tissues (jaitin et al., ). a refined clustering method called pcareduce (zurauskiene and yau, ) was designed for scrna-seq. it iteratively uses pca combined with k-means to produce the hierarchical tree of the cells. for distance metrics employed […]

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pcaReduce institution(s)
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK
pcaReduce funding source(s)
The authors are supported by a Wellcome Trust Core Award Grant Number 090532/Z/09/Z, the Li Ka Shing Foundation Oxford-Stanford Big Data for Human Health Seed Grant and a UK Medical Research Council New Investigator Research Grant (Ref. No. MR/L001411/1).

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