Package: Oscope 1.43.0

Ning Leng

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.

Authors:Ning Leng

Oscope_1.43.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Oscope/json (API)

# Install 'Oscope' in R:

install.packages('Oscope', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

OscopeExampleData - Simulated gene level data set with 600 genes and 30 cells.

On BioConductor:Oscope-1.43.0(bioc 3.24)Oscope-1.42.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology statisticalmethod rnaseq sequencing geneexpression

5.03 score 1 packages 18 scripts 492 downloads 11 mentions 17 exports 45 dependencies

Last updated from:4944b6cdfc. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	160
linux-devel-x86_64	NOTE	262
source / vignettes	OK	285
linux-release-x86_64	NOTE	247
macos-release-arm64	NOTE	120
macos-oldrel-arm64	NOTE	88
windows-devel	NOTE	128
windows-release	NOTE	179
windows-oldrel	NOTE	138
wasm-release	OK	126

Exports:AbsCor CalcMV FlagCluster FormatSineOut ImpShift NISFun NormForSine Opt2Shift OscopeENI OscopeKM OscopeSine PermuCut PipeR PipeShiftCDF scanK SineFun SineOptim

Dependencies:BH BiocParallel bitops blockmodeling brio callr caTools cli cluster codetools cpp11 crayon desc diffobj EBSeq evaluate formatR fs futile.logger futile.options glue gplots gtools jsonlite KernSmooth lambda.r lattice lifecycle magrittr Matrix otel pkgbuild pkgload praise processx ps R6 Rcpp RcppEigen rlang rprojroot snow testthat waldo withr

Oscope_vigette

1 Introduction | 2 Run Oscope | 3 Session info

Rendered fromOscope_vignette.Rnwusingutils::Sweave

Last update: 2015-07-30
Started: 2015-07-30

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

Package: Oscope 1.43.0

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

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