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.

Author
Bo Wang [aut], Daniele Ramazzotti [aut, cre], Luca De Sano [aut], Junjie Zhu [ctb], Emma Pierson [ctb], Serafim Batzoglou [ctb]
Date of publication
None
Maintainer
Daniele Ramazzotti <daniele.ramazzotti@yahoo.com>
License
file LICENSE
Version
1.0.1
URLs

View on Bioconductor

Man pages

BuettnerFlorian
test dataset
SIMLR
SIMLR
SIMLR_Feature_Ranking
SIMLR Feature Ranking

Files in this package

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