NULISAseq R package v1.2
- R (version 4.4+)
- Run the following R code (typical installation time < 5 minutes):
install.packages('devtools')
devtools::install_github('Alamar-Biosciences/NULISAseqR',
ref = 'main'
)
- Load the package in R with
library(NULISAseqR).
# Load the NULISAseqR library
library(NULISAseqR)
# This is an input XML file example that is included with NULISAseqR. You could
# alternatively change the variable inputFile to be one of your own XML files,
# e.g. inputFile <- "filename.xml"
inputFile <- paste0(
dirname(system.file("rmarkdown/templates/nulisaseq/skeleton", "skeleton.Rmd", package="NULISAseqR")),
"/detectability_P1_Tr03.xml"
)
# Load the XML data
dataXML <- loadNULISAseq(inputFile)
# Load the NULISAseqR library
library(NULISAseqR)
# Load the XLSX data where "XLSX inputFile" is the name of your XLSX file
dataXLSX <- readNULISAseq("XLSX inputFile", file_type="xlsx") # example of loading an XLSX file
Run the following to generate a QC report ( < 5 minutes)
# Location of QC report template included with NULISAseqR
template <- system.file("rmarkdown/templates/nulisaseq/skeleton", "skeleton.Rmd", package="NULISAseqR")
# Command to create the QC report (Note that QC reports can only be created using XML files)
rmarkdown::render(
template,
output_file = "~/output.html",
params = list(
dataDir = dirname(template),
xmlFiles = c("detectability_P1_Tr03.xml")
)
)