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.

Author
Aaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb]
Date of publication
None
Maintainer
Aaron Lun <alun@wehi.edu.au>
License
GPL-3
Version
1.2.0

View on Bioconductor

Man pages

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
DM
Compute the distance-to-median statistic
quickCluster
Quick clustering of cells
sandbag
Cell cycle phase training
selectorPlot
Construct a selector plot via Shiny
spikes
Construct the spike-in matrix
technicalCV2
Model the technical coefficient of variation
testVar
Test for significantly large variances
trendVar
Fit a variance trend

Files in this package

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/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