Oscope
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see Oscope.
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Bioconductor version: 3.15
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("Oscope")
):
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")
Oscope_vigette | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod |
Version | 1.26.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
License | Artistic-2.0 |
Depends | EBSeq, cluster, testthat, BiocParallel |
Imports | |
System Requirements | |
URL |
See More
Suggests | BiocStyle |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
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Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | Oscope_1.26.0.tar.gz |
Windows Binary | Oscope_1.26.0.zip |
macOS Binary (x86_64) | Oscope_1.26.0.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 |
Old Source Packages for BioC 3.15 | Source Archive |