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Oscope

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("Oscope")):

Installation

To install this package, start R (version "4.3") 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")
Oscope_vigette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod
Version 1.32.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License Artistic-2.0
Depends EBSeq, cluster, testthat, BiocParallel
Imports
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Imports Me scDDboost
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Package Archives

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

Source Package Oscope_1.32.0.tar.gz
Windows Binary Oscope_1.32.0.zip
macOS Binary (x86_64) Oscope_1.32.0.tgz
macOS Binary (arm64) Oscope_1.32.0.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