SEPA
This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SEPA.
SEPA
Bioconductor version: 3.8
Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.
Author: Zhicheng Ji, Hongkai Ji
Maintainer: Zhicheng Ji <zji4 at jhu.edu>
citation("SEPA")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SEPA")
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("SEPA")| SEPA: Single-Cell Gene Expression Pattern Analysis | R Script | |
| Reference Manual |
Details
| biocViews | GO, GUI, GeneExpression, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | GPL(>=2) |
| Depends | R (>= 2.10.0) |
| Imports | ggplot2, shiny, topGO, segmented, reshape2, org.Hs.eg.db, org.Mm.eg.db |
| System Requirements | |
| URL |
See More
| Suggests | knitr |
| Linking To | |
| 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 | SEPA_1.12.0.tar.gz |
| Windows Binary | SEPA_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | SEPA_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SEPA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SEPA |
| Bioc Package Browser | https://code.bioconductor.org/browse/SEPA/ |
| Package Short Url | https://bioconductor.org/packages/SEPA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |