SEPA

DOI: 10.18129/B9.bioc.SEPA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SEPA.

SEPA

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	SEPA: Single-Cell Gene Expression Pattern Analysis
PDF		Reference Manual

Details

biocViews	GO, GUI, GeneExpression, Software, Visualization
Version	1.13.0
In Bioconductor since	BioC 3.2 (R-3.2) (4 years)
License	GPL(>=2)
Depends	R (>= 2.10.0)
Imports	ggplot2, shiny, topGO, segmented, reshape2, org.Hs.eg.db, org.Mm.eg.db
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SEPA_1.13.0.tar.gz
Windows Binary	SEPA_1.13.0.zip
Mac OS X 10.11 (El Capitan)	SEPA_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SEPA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SEPA
Package Short Url	https://bioconductor.org/packages/SEPA/
Package Downloads Report	Download Stats