brainImageR

DOI: 10.18129/B9.bioc.brainImageR    

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 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see brainImageR.

A Framework for visualizing gene set enrichment throughout neurodevelopment

Bioconductor version: Release (3.10)

BrainImageR is a package that provides the user with information of where in the human brain their gene set corresponds to. This is provided both as a continuous variable and as a easily-interpretable image. BrainImageR has additional functionality of identifying approximately when in developmental time that a gene expression dataset corresponds to. Both the spatial gene set enrichment and the developmental time point prediction are assessed in comparison to the Allen Brain Atlas reference data.

Author: Sara Linker [aut, cre]

Maintainer: Sara B Linker <sara.linker at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("brainImageR")

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

Documentation

PDF		Reference Manual

Details

biocViews	GeneExpression, GenePrediction, GeneSetEnrichment, Software, Transcription
Version	1.4.0
In Bioconductor since	BioC 3.8 (R-3.5) (1.5 years)
License	CC BY-SA 4.0
Depends	R (>= 3.5)
Imports	BiocGenerics, ExperimentHub, ggplot2, grDevices, grid, gridExtra, methods, randomForest, RColorBrewer, stats, testthat
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/saralinker/brainImageR
BugReports	https://github.com/saralinker/brainImageR/issues
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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/brainImageR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/brainImageR
Package Short Url	https://bioconductor.org/packages/brainImageR/
Package Downloads Report	Download Stats