brainImageR

DOI: 10.18129/B9.bioc.brainImageR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see brainImageR.

A Framework for visualizing gene set enrichment throughout neurodevelopment

Bioconductor version: 3.9

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("brainImageR")

 

HTML	R Script	brainImageR
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GenePrediction, GeneSetEnrichment, Software, Transcription
Version	1.1.0
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	brainImageR_1.1.0.tar.gz
Windows Binary	brainImageR_1.1.0.zip
Mac OS X 10.11 (El Capitan)	brainImageR_1.1.0.tgz
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