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("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 | ||
| 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 [email protected]: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 |