scde
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scde.
Single Cell Differential Expression
Bioconductor version: 3.11
The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).
Author: Peter Kharchenko [aut, cre], Jean Fan [aut]
Maintainer: Jean Fan <jeanfan at fas.harvard.edu>
citation("scde")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scde")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Bayesian, DifferentialExpression, ImmunoOncology, RNASeq, Software, StatisticalMethod, Transcription |
| Version | 2.16.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.0), flexmix |
| Imports | Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel |
| System Requirements | |
| URL | http://pklab.med.harvard.edu/scde |
| Bug Reports | https://github.com/hms-dbmi/scde/issues |
See More
| Suggests | knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scde_2.16.0.tar.gz |
| Windows Binary | scde_2.16.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | scde_2.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scde |
| Source Repository (Developer Access) | git clone [email protected]:packages/scde |
| Bioc Package Browser | https://code.bioconductor.org/browse/scde/ |
| Package Short Url | https://bioconductor.org/packages/scde/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |