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

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.

Author
Ning Leng
Date of publication
None
Maintainer
Ning Leng <lengning1@gmail.com>
License
Artistic-2.0
Version
1.4.0

View on Bioconductor

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

Files in this package

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