SEPA

DOI: 10.18129/B9.bioc.SEPA    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of SEPA; to use it, please install the devel version of Bioconductor.

SEPA

Bioconductor version: Development (3.10)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SEPA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews GO, GUI, GeneExpression, Software, Visualization
Version 1.15.1
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
Windows Binary
Mac OS X 10.11 (El Capitan)
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/
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