scran: Methods for Single-Cell RNA-Seq Data Analysis
Version 1.4.4

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.

Browse man pages Browse package API and functions Browse package files

AuthorAaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb], Laleh Haghverdi [ctb]
Bioconductor views BatchEffect GeneExpression Normalization RNASeq Sequencing SingleCell Software Transcriptomics Visualization
Date of publicationNone
MaintainerAaron Lun <alun@wehi.edu.au>
LicenseGPL-3
Version1.4.4
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("scran")

Man pages

buildSNNGraph: Build a SNN graph
combineVar: Combine variance decompositions
computeSpikeFactors: Normalization with spike-in counts
computeSumFactors: Normalization by deconvolution
convertTo: Convert to other classes
correlatePairs: Test for significant correlations
cyclone: Cell cycle phase classification
decomposeVar: Decompose the gene-level variance
denoisePCA: Denoise expression with PCA
DM: Compute the distance-to-median statistic
exploreData: Shiny app for explorative data analysis
findMarkers: Find marker genes
improvedCV2: Stably model the technical coefficient of variation
mnnCorrect: Mutual nearest neighbors correction
overlapExprs: Overlap expression profiles
quickCluster: Quick clustering of cells
sandbag: Cell cycle phase training
selectorPlot: Construct a selector plot via Shiny
spikes: Set spike-in rows
technicalCV2: Model the technical coefficient of variation
testVar: Test for significantly large variances
trendVar: Fit a variance trend

Functions

DM Man page Source code
buildSNNGraph Man page Source code
buildSNNGraph,SCESet-method Man page
buildSNNGraph,matrix-method Man page
check_centered_SF Source code
choose_gene_names Source code
combineVar Man page Source code
computeSpikeFactors Man page
computeSpikeFactors,SCESet-method Man page
computeSumFactors Man page Source code
computeSumFactors,SCESet-method Man page
computeSumFactors,matrix-method Man page
construct_pair_indices Source code
convertTo Man page
convertTo,SCESet-method Man page
correlateNull Man page Source code
correlatePairs Man page
correlatePairs,SCESet-method Man page
correlatePairs,matrix-method Man page
correlate_pairs Source code
cosine.norm Source code
create_linear_system Source code
cyclone Man page
cyclone,SCESet-method Man page
cyclone,matrix-method Man page
decomposeVar Man page
decomposeVar,SCESet,list-method Man page
decomposeVar,matrix,list-method Man page
denoisePCA Man page Source code
denoisePCA,SCESet-method Man page
denoisePCA,matrix-method Man page
exploreData Man page Source code
find.markers Source code
find.mutual.nn Source code
find.shared.subspace Source code
findMarkers Man page Source code
findMarkers,SCESet-method Man page
findMarkers,matrix-method Man page
generatePlot1 Source code
generatePlot2 Source code
generateSphere Source code
get.bio.span Source code
get_correlation Source code
get_nls_starts Source code
get_phase_score Source code
improvedCV2 Man page
improvedCV2,SCESet-method Man page
improvedCV2,matrix-method Man page
isSpike<- Man page
isSpike<-,SCESet-method Man page
makeVarDefaults Source code
mnnCorrect Man page Source code
mprovedCV2 Source code
overlapExprs Man page Source code
overlapExprs,SCESet-method Man page
overlapExprs,matrix-method Man page
prepare_cv2_data Source code
quantile.trend Source code
quickCluster Man page
quickCluster,SCESet-method Man page
quickCluster,matrix-method Man page
resetValues Source code
sOneWay Source code
s_sig_limited Source code
sandbag Man page
sandbag,SCESet-method Man page
sandbag,matrix-method Man page
selectorPlot Man page Source code
spikeSubset Source code
subset_to_index Source code
technicalCV2 Man page Source code
technicalCV2,SCESet-method Man page
technicalCV2,matrix-method Man page
testVar Man page Source code
trendVar Man page
trendVar,SCESet-method Man page
trendVar,matrix-method Man page
trend_var Source code
workerAssign Source code

Files

DESCRIPTION
NAMESPACE
R
R/DM.R
R/buildSNNGraph.R
R/combineVar.R
R/computeSpikeFactors.R
R/computeSumFactors.R
R/convertTo.R
R/correlateNull.R
R/correlatePairs.R
R/cyclone.R
R/decomposeVar.R
R/denoisePCA.R
R/exploreData.R
R/findMarkers.R
R/improvedCV2.R
R/mnnCorrect.R
R/overlapExprs.R
R/quickCluster.R
R/sandbag.R
R/selectorPlot.R
R/technicalCV2.R
R/testVar.R
R/trendVar.R
R/utils.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/scran.R
inst/doc/scran.Rmd
inst/doc/scran.html
inst/exdata
inst/exdata/generate_markers.R
inst/exdata/human_cycle_markers.rds
inst/exdata/mouse_cycle_markers.rds
man
man/DM.Rd
man/buildSNNGraph.Rd
man/combineVar.Rd
man/computeSpikeFactors.Rd
man/computeSumFactors.Rd
man/convertTo.Rd
man/correlatePairs.Rd
man/cyclone.Rd
man/decomposeVar.Rd
man/denoisePCA.Rd
man/exploreData.Rd
man/findMarkers.Rd
man/improvedCV2.Rd
man/mnnCorrect.Rd
man/overlapExprs.Rd
man/quickCluster.Rd
man/sandbag.Rd
man/selectorPlot.Rd
man/spikes.Rd
man/technicalCV2.Rd
man/testVar.Rd
man/trendVar.Rd
src
src/Makevars
src/build_snn.cpp
src/compute_CV2.cpp
src/compute_cordist.cpp
src/compute_rho.cpp
src/estimate_variance.cpp
src/forge_system.cpp
src/init.cpp
src/matrix_info.cpp
src/overlap_exprs.cpp
src/run_dormqr.cpp
src/scran.h
src/shuffle_scores.cpp
src/utils.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test-convert.R
tests/testthat/test-correlate.R
tests/testthat/test-cyclone.R
tests/testthat/test-denoise.R
tests/testthat/test-markers.R
tests/testthat/test-methods.R
tests/testthat/test-normalize.R
tests/testthat/test-overlap.R
tests/testthat/test-sandbag.R
tests/testthat/test-shuffle.R
tests/testthat/test-snn.R
tests/testthat/test-technical.R
tests/testthat/test-variance.R
vignettes
vignettes/scran.Rmd
scran documentation built on May 24, 2017, 2 a.m.