BrainSABER

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see BrainSABER.

Brain Span Atlas in Biobase Expressionset R toolset


Bioconductor version: 3.14

The Allen Institute for Brain Science provides an RNA sequencing (RNA-Seq) data resource for studying transcriptional mechanisms involved in human brain development known as BrainSpan. BrainSABER is an R package that facilitates comparison of user data with the various developmental stages and brain structures found in the BrainSpan atlas by generating dynamic similarity heatmaps for the two data sets. It also provides a self-validating container for user data.

Author: Carrie Minette [aut], Evgeni Radichev [aut], USD Biomedical Engineering [aut, cre]

Maintainer: USD Biomedical Engineering <bicbioeng at gmail.com>

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

Installation

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


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

BiocManager::install("BrainSABER")

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("BrainSABER")
BrainSABER HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Sequencing, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.1.0), biomaRt, SummarizedExperiment
Imports data.table, lsa, methods, S4Vectors, utils, BiocFileCache, shiny
System Requirements
URL
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Suggests BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr, plotly, rmarkdown
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package BrainSABER_1.4.0.tar.gz
Windows Binary BrainSABER_1.4.0.zip
macOS 10.13 (High Sierra) BrainSABER_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BrainSABER
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BrainSABER
Bioc Package Browser https://code.bioconductor.org/browse/BrainSABER/
Package Short Url https://bioconductor.org/packages/BrainSABER/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive