BrainSABER
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see BrainSABER.
Brain Span Atlas in Biobase Expressionset R toolset
Bioconductor version: 3.16
The Allen Institute for Brain Science provides an RNA sequencing (RNA-Seq) data resource for studying transcriptional mechanisms involved in human brain development known as BrainSpan. BrainSABER is an R package that facilitates comparison of user data with the various developmental stages and brain structures found in the BrainSpan atlas by generating dynamic similarity heatmaps for the two data sets. It also provides a self-validating container for user data.
Author: Carrie Minette [aut], Evgeni Radichev [aut], USD Biomedical Engineering [aut, cre]
Maintainer: USD Biomedical Engineering <bicbioeng at gmail.com>
citation("BrainSABER")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BrainSABER")
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("BrainSABER")| BrainSABER | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Sequencing, Software, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), biomaRt, SummarizedExperiment |
| Imports | data.table, lsa, methods, S4Vectors, utils, BiocFileCache, shiny |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr, plotly, 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 | BrainSABER_1.8.0.tar.gz |
| Windows Binary | BrainSABER_1.8.0.zip |
| macOS Binary (x86_64) | BrainSABER_1.8.0.tgz |
| macOS Binary (arm64) | BrainSABER_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BrainSABER |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BrainSABER |
| Package Short Url | https://bioconductor.org/packages/BrainSABER/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |