SIMLR: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning

Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical to identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. SIMLR is capable of separating known subpopulations more accurately in single-cell data sets than do existing dimension reduction methods. Additionally, SIMLR demonstrates high sensitivity and accuracy on high-throughput peripheral blood mononuclear cells (PBMC) data sets generated by the GemCode single-cell technology from 10x Genomics.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SIMLR")
AuthorBo Wang [aut], Daniele Ramazzotti [aut, cre], Luca De Sano [aut], Junjie Zhu [ctb], Emma Pierson [ctb], Serafim Batzoglou [ctb]
Bioconductor views Clustering GeneExpression Sequencing SingleCell
Date of publicationNone
MaintainerDaniele Ramazzotti <daniele.ramazzotti@yahoo.com>
Licensefile LICENSE
Version1.0.1
https://github.com/BatzoglouLabSU/SIMLR

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Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/SIMLR.R R/SIMLR_Feature_Ranking.R R/compute.multiple.kernel.R R/data.R R/network.diffusion.R R/tsne.R R/utils.simlr.R R/zzz.R
build
build/vignette.rds
data
data/BuettnerFlorian.RData
data/datalist
inst
inst/doc
inst/doc/SIMLR.R
inst/doc/SIMLR.Rnw
inst/doc/SIMLR.pdf
man
man/BuettnerFlorian.Rd man/SIMLR.Rd man/SIMLR_Feature_Ranking.Rd
src
src/projsplx_R.c
tests
tests/testthat
tests/testthat.R tests/testthat/test_simlr.R
vignettes
vignettes/SIMLR.Rnw

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