Oscope
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.36.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 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 | scDDboost |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Oscope_1.36.0.tar.gz |
| Windows Binary (x86_64) | Oscope_1.36.0.zip |
| macOS Binary (x86_64) | Oscope_1.36.0.tgz |
| macOS Binary (arm64) | Oscope_1.35.0.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 |