SEtools

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see SEtools.

SEtools: tools for working with SummarizedExperiment

Bioconductor version: 3.14

This includes a set of tools for working with the SummarizedExperiment class, including merging, melting, aggregation and plotting functions. In particular, SEtools offers a simple interface for plotting complex heatmaps from SE objects.

Author: Pierre-Luc Germain [cre, aut]

Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("SEtools")

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("SEtools")

SEtools HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, Software, Visualization

Version 1.8.0

In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)

License GPL

Depends R (>= 4.0)

Imports S4Vectors, SummarizedExperiment, data.table, seriation, ComplexHeatmap, circlize, methods, BiocParallel, randomcoloR, edgeR, openxlsx, sva, stats, DESeq2, Matrix, grid

System Requirements

URL

Bug Reports https://github.com/plger/SEtools

Suggests BiocStyle, knitr, rmarkdown, ggplot2, pheatmap

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 SEtools_1.8.0.tar.gz

Windows Binary SEtools_1.8.0.zip

macOS 10.13 (High Sierra) SEtools_1.8.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SEtools

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SEtools

Bioc Package Browser https://code.bioconductor.org/browse/SEtools/

Package Short Url https://bioconductor.org/packages/SEtools/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive