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 is the development version of brainImageR; to use it, please install the devel version of Bioconductor.

A Framework for visualizing gene set enrichment throughout neurodevelopment

Bioconductor version: Development (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>

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

Installation

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

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

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

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 1.3.1
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
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
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
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/
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