Oscope

DOI: 10.18129/B9.bioc.Oscope  

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

Bioconductor version: Release (3.16)

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

Maintainer: Ning Leng <lengning1 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Oscope")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Oscope")

 

PDF	R Script	Oscope_vigette
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod
Version	1.28.0
In Bioconductor since	BioC 3.2 (R-3.2) (7.5 years)
License	Artistic-2.0
Depends	EBSeq, cluster, testthat, BiocParallel
Imports
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	scDDboost
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Oscope_1.28.0.tar.gz
Windows Binary	Oscope_1.28.0.zip
macOS Binary (x86_64)	Oscope_1.28.0.tgz
macOS Binary (arm64)	Oscope_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Oscope
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Oscope
Bioc Package Browser	https://code.bioconductor.org/browse/Oscope/
Package Short Url	https://bioconductor.org/packages/Oscope/
Package Downloads Report	Download Stats