BrainSABER

DOI: 10.18129/B9.bioc.BrainSABER  

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

This package is for version 3.16 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: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	BrainSABER
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Sequencing, Software, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), biomaRt, SummarizedExperiment
Imports	data.table, lsa, methods, S4Vectors, utils, BiocFileCache, shiny
LinkingTo
Suggests	BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr, plotly, rmarkdown
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	BrainSABER_1.8.0.tar.gz
Windows Binary	BrainSABER_1.8.0.zip
macOS Binary (x86_64)	BrainSABER_1.8.0.tgz
macOS Binary (arm64)	BrainSABER_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BrainSABER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BrainSABER
Package Short Url	https://bioconductor.org/packages/BrainSABER/
Package Downloads Report	Download Stats