brainImageR

DOI: 10.18129/B9.bioc.brainImageR    

A Framework for visualizing gene set enrichment throughout neurodevelopment

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("brainImageR", version = "3.8")

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 1.0.0
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_1.0.0.tar.gz
Windows Binary brainImageR_1.0.0.zip
Mac OS X 10.11 (El Capitan) brainImageR_1.0.0.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 http://bioconductor.org/packages/brainImageR/
Package Downloads Report Download Stats

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