brainImageR

This package is for version 3.9 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: 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>

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

Installation

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


if (!require("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")
brainImageR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GenePrediction, GeneSetEnrichment, Software, Transcription
Version 1.1.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License CC BY-SA 4.0
Depends R (>= 3.5)
Imports BiocGenerics, ExperimentHub, ggplot2, grDevices, grid, gridExtra, methods, randomForest, RColorBrewer, stats, testthat
System Requirements
URL https://github.com/saralinker/brainImageR
Bug Reports https://github.com/saralinker/brainImageR/issues
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/brainImageR/
Package Short Url https://bioconductor.org/packages/brainImageR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive