Oscope: Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Version 1.6.0

Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.

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AuthorNing Leng
Bioconductor views GeneExpression RNASeq Sequencing StatisticalMethod
Date of publicationNone
MaintainerNing Leng <lengning1@gmail.com>
LicenseArtistic-2.0
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Oscope")

Man pages

AbsCor: Calculate absolute correlations among gene pairs
CalcMV: Calculate estimated mean and variance of RNA-Seq data
FlagCluster: Flag gene clusters with small within-cluster phase...
FormatSineOut: Format SinFun outputs from lists to matrix
ImpShift: Search for the optimal sample order by using the Extended...
NISFun: Run Extended Nearest Insertion and 2-opt on a gene cluster...
NormForSine: Rescale the gene/isoform expression matrix
Opt2Shift: Run the 2-opt algorithm to improve the optimal order...
OscopeENI: Search for the optimal sample order for different gene...
OscopeExampleData: Simulated gene level data set with 600 genes and 30 cells.
OscopeKM: Oscope K medoid module
Oscope-package: Oscope - A statistical pipeline for identifying oscillatory...
OscopeSine: Apply sine model on the full set of genes or isoforms
PermuCut: Define sine scroe cutoff using permuted data
PipeR: Calculate residual of polynomial fit
PipeShiftCDF: Calculate residual of the sliding polynomial regression
scanK: Run k-medoid algorithm with varying k on similarity matrix
SineFun: Apply sine model on one particular gene vs. other genes
SineOptim: Function for searching optimal phase shift

Functions

AbsCor Man page Source code
CalcMV Man page Source code
FlagCluster Man page Source code
FormatSineOut Man page Source code
ImpShift Man page Source code
NISFun Man page Source code
NormForSine Man page Source code
Opt2Shift Man page Source code
Oscope Man page
Oscope-package Man page
OscopeENI Man page Source code
OscopeExampleData Man page
OscopeKM Man page Source code
OscopeSine Man page Source code
PermuCut Man page Source code
PipeR Man page Source code
PipeShiftCDF Man page Source code
SineFun Man page Source code
SineOptim Man page Source code
scanK Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AbsCor.R
R/CalcMV.R
R/FlagCluster.R
R/FormatSineOut.R
R/ImpShift.R
R/NISFun.R
R/NormForSine.R
R/Opt2Shift.R
R/OscopeENI.R
R/OscopeKM.R
R/OscopeSine.R
R/PermuCut.R
R/PipeR.R
R/PipeShiftCDF.R
R/SineFun.R
R/SineOptim.R
R/scanK.R
build
build/vignette.rds
data
data/OscopeExampleData.rda
demo
demo/00Index
demo/Oscope.R
inst
inst/doc
inst/doc/Oscope_vignette.R
inst/doc/Oscope_vignette.Rnw
inst/doc/Oscope_vignette.pdf
man
man/AbsCor.Rd
man/CalcMV.Rd
man/FlagCluster.Rd
man/FormatSineOut.Rd
man/ImpShift.Rd
man/NISFun.Rd
man/NormForSine.Rd
man/Opt2Shift.Rd
man/Oscope-package.Rd
man/OscopeENI.Rd
man/OscopeExampleData.Rd
man/OscopeKM.Rd
man/OscopeSine.Rd
man/PermuCut.Rd
man/PipeR.Rd
man/PipeShiftCDF.Rd
man/SineFun.Rd
man/SineOptim.Rd
man/scanK.Rd
vignettes
vignettes/Oscope_vignette.Rnw
vignettes/Pipe.pdf
vignettes/lengetal.bib
vignettes/natbib.bst
vignettes/natbib.sty
Oscope documentation built on May 20, 2017, 9:14 p.m.