SIMLR: Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Version 1.2.1

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.

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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
Version1.2.1
URL https://github.com/BatzoglouLabSU/SIMLR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SIMLR")

Man pages

BuettnerFlorian: test dataset for SIMLR
SIMLR: SIMLR
SIMLR_Feature_Ranking: SIMLR Feature Ranking
SIMLR_Large_Scale: SIMLR Large Scale
ZeiselAmit: test dataset for SIMLR large scale

Functions

BuettnerFlorian Man page
Rtsne Source code
Rtsne_cpp Source code
SIMLR Man page
SIMLR_Feature_Ranking Man page
SIMLR_Large_Scale Man page
ZeiselAmit Man page
onUnload Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/RcppExports.R
R/Rtsne.R
R/SIMLR.R
R/SIMLR_Feature_Ranking.R
R/SIMLR_Large_Scale.R
R/compute.multiple.kernel.R
R/data.R
R/network.diffusion.R
R/tsne.R
R/utils.simlr.R
R/utils.simlr.large.scale.R
R/zzz.R
build
build/vignette.rds
data
data/BuettnerFlorian.RData
data/ZeiselAmit.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
man/SIMLR_Large_Scale.Rd
man/ZeiselAmit.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/Rtsne.cpp
src/projsplx_R.c
src/sptree.cpp
src/sptree.h
src/tsne.cpp
src/tsne.h
src/vptree.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test_simlr.R
vignettes
vignettes/SIMLR.Rnw
SIMLR documentation built on May 20, 2017, 10:24 p.m.