BrainSABER

DOI: 10.18129/B9.bioc.BrainSABER    

This is the development version of BrainSABER; for the stable release version, see BrainSABER.

Brain Span Atlas in Biobase Expressionset R toolset

Bioconductor version: Development (3.15)

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 <carrie.minette at coyotes.usd.edu>, Evgeni Radichev <evgeni.radichev at usd.edu>, USD Biomedical Engineering <bicbioeng at gmail.com>

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

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

Installation

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

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

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

BiocManager::install("BrainSABER")

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

Documentation

PDF   Reference Manual

Details

biocViews GeneExpression, Sequencing, Software, Visualization
Version 1.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
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
Windows Binary
macOS 10.13 (High Sierra)
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/
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