SEPA

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

Citation (from within R, enter citation("SEPA")):

Installation

To install this package, start R (version "3.6") 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 PDF R Script
Reference Manual PDF

Details

biocViews GO, GUI, GeneExpression, Software, Visualization
Version 1.13.0
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
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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
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 3.9 Source Archive