Oscope
This is the released version of Oscope; for the devel version, see Oscope.
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.42.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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_1.42.0.tar.gz |
| Windows Binary (x86_64) | Oscope_1.42.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Oscope_1.42.0.tgz |
| macOS Binary (sonoma-arm64) | Oscope_1.42.0.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 |