hcstubbe / genefindr

A program for finding occurrences of gene identifiers and synonyms in PubMed listed abstracts and linking them to gene sets (e..g. lists from differential gene experssion)

genefindr

Genefindr is currently converted into a Shiny app.

Example

# 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)