csf-ngs / forskaller

simple small API for our superior in house LIMS built by Heinz

forskaller

small R API client for our superior in house LIMS built by Heinz

install

library("devtools")
install_github("forskaller", "csf-ngs")

example usage

sample info

library("forskaller")

username <- ""
password <- ""
multiplex <- 0


session <- startSession(createCredentials(username, password))
m <- getMultiplex(multiplex, session)
samples <- getSamples(m$sampleId, session)
samples
samples$measurements$Preparation
samples$measurements$`cDNA Synthesis`
endSession(session)

demultiplexing

illumina2bam has to be installed and java -jar /path/to/BamIndexDecoder.jar has to be aliased to BamIndexDecoder

library("forskaller")
username <- ""
password <- ""

session <- startSession(createCredentials(username, password))
cmd <- generateSplitFile(bamPath, session)
print(cmd)
endSession(session)