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Welcome to the BrainStars-for-R wiki!
The BrainStars for R package can search and get gene expression data and some kind of plots from BrainStars (B*). BrainStars is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. The BrainStars database has a REST API to query gene expression data, annotations and some kind of figures written by Dr. Takeya Kasukawa. This package is wrapper for BrainStars REST API in R. BrainStars gene expression data, images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License.
BrainStars is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.
For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2).
These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database.
##Install $ sudo R > install.packages("RJSONIO") > install.packages("RCurl") > source("http://bioconductor.org/biocLite.R") > biocLite() > q()
$ curl -O https://github.com/dritoshi/BrainStars-for-R/blob/master/brainstars_0.99.3.tar.gz
$ sudo R CMD INSTALL brainstars-0.99.3.tar.gz
The BrainStars for R package was accepted Bioconductor. In near future, you will install the package using by biocLite().
$ sudo R
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("BrainStars")
> q()
##Usage See vignette (pdf).
library("brainstars")
# Search API
> my.genes <- getBrainStars(query = "receptor/10,5", type = "search")
> my.genes.json <- getBrainStars(query = "receptor/10,5", type = "search", json = TRUE)
> my.genes.count <- getBrainStars(query = "receptor/count", type = "search")
# Marker API
> my.marker <- getBrainStars(query = "high/LS/count", type = "marker")
# Expression API
> my.gene.exprs <- getBrainStars(query = c("1439627_at"), type = "expression")
> my.gene.exprs
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1 features, 102 samples
element names: exprs
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
# Graph API
> getBrainStarsFigure("1439627_at", "exprgraph", "png")
# Graph API
> getBrainStarsFigure("1439627_at", "exprmap", "png")
# Graph API
> getBrainStarsFigure("1439627_at", "switchhist", "png")
