Genefindr is currently converted into a Shiny app.
# Select abstract files
abstractFileNames = c("hiv 110422.txt",
"bcells 28793.txt",
"tcells 84002.txt")
names(abstractFileNames) = abstractFileNames
# Run genefindr for counting occurrences
runGeneFindr(abstractFileNames,
n.cores = 1, # to run on widonws
chunks = 10, # number of chunks needs to be smaller or equal to number of investigated genes
GEOsearchFile = "files/result.strict.brisbane.basel.durham.csv" # investigate only sex biased genes
)
# Count numbers of abstracts
lapply(abstractFileNames, count.abstracts)