scran: Methods for Single-Cell RNA-Seq Data Analysis

Implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

AuthorAaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb]
Date of publicationNone
MaintainerAaron Lun <alun@wehi.edu.au>
LicenseGPL-3
Version1.2.2

View on Bioconductor

Functions

computeSpikeFactors Man page
computeSpikeFactors,SCESet-method Man page
computeSumFactors Man page
computeSumFactors,matrix-method Man page
computeSumFactors,SCESet-method Man page
convertTo Man page
convertTo,SCESet-method Man page
correlateNull Man page
correlatePairs Man page
correlatePairs,matrix-method Man page
correlatePairs,SCESet-method Man page
cyclone Man page
cyclone,matrix-method Man page
cyclone,SCESet-method Man page
decomposeVar Man page
decomposeVar,matrix,list-method Man page
decomposeVar,SCESet,list-method Man page
DM Man page
isSpike Man page
isSpike<- Man page
isSpike<-,SCESet,character-method Man page
isSpike,SCESet-method Man page
isSpike<-,SCESet,NULL-method Man page
quickCluster Man page
quickCluster,matrix-method Man page
quickCluster,SCESet-method Man page
sandbag Man page
sandbag,matrix-method Man page
sandbag,SCESet-method Man page
selectorPlot Man page
spikes Man page
spikes,SCESet-method Man page
technicalCV2 Man page
technicalCV2,matrix-method Man page
technicalCV2,SCESet-method Man page
testVar Man page
trendVar Man page
trendVar,matrix-method Man page
trendVar,SCESet-method Man page

Files

scran/DESCRIPTION
scran/NAMESPACE
scran/R
scran/R/DM.R scran/R/computeSpikeFactors.R scran/R/computeSumFactors.R scran/R/convertTo.R scran/R/correlatePairs.R scran/R/cyclone.R scran/R/decomposeVar.R scran/R/quickCluster.R scran/R/sandbag.R scran/R/selectorPlot.R scran/R/technicalCV2.R scran/R/trendVar.R scran/R/utils.R
scran/build
scran/build/vignette.rds
scran/inst
scran/inst/CITATION
scran/inst/NEWS.Rd
scran/inst/doc
scran/inst/doc/scran.R
scran/inst/doc/scran.Rmd
scran/inst/doc/scran.html
scran/inst/exdata
scran/inst/exdata/generate_markers.R
scran/inst/exdata/human_cycle_markers.rds
scran/inst/exdata/mouse_cycle_markers.rds
scran/man
scran/man/DM.Rd scran/man/computeSpikeFactors.Rd scran/man/computeSumFactors.Rd scran/man/convertTo.Rd scran/man/correlatePairs.Rd scran/man/cyclone.Rd scran/man/decomposeVar.Rd scran/man/quickCluster.Rd scran/man/sandbag.Rd scran/man/selectorPlot.Rd scran/man/spikes.Rd scran/man/technicalCV2.Rd scran/man/testVar.Rd scran/man/trendVar.Rd
scran/src
scran/src/Makevars
scran/src/compute_CV2.cpp
scran/src/compute_cordist.cpp
scran/src/compute_rho.cpp
scran/src/estimate_variance.cpp
scran/src/forge_system.cpp
scran/src/init.cpp
scran/src/matrix_info.cpp
scran/src/run_dormqr.cpp
scran/src/scran.h
scran/src/shuffle_scores.cpp
scran/src/utils.h
scran/tests
scran/tests/testthat
scran/tests/testthat.R
scran/tests/testthat/test-convert.R
scran/tests/testthat/test-correlate.R
scran/tests/testthat/test-cyclone.R
scran/tests/testthat/test-methods.R
scran/tests/testthat/test-normalize.R
scran/tests/testthat/test-sandbag.R
scran/tests/testthat/test-shuffle.R
scran/tests/testthat/test-technical.R
scran/tests/testthat/test-variance.R
scran/vignettes
scran/vignettes/scran.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.