descide: Run DeSciDe pipeline

In DeSciDe: Tool for Unbiased Literature Searching and Gene List Curation

Run DeSciDe pipeline

Description

Run the entire analysis pipeline including PubMed search, STRING database search, and plotting.

Usage

descide(
  genes_list,
  terms_list,
  rank_method = "weighted",
  species = 9606,
  network_type = "full",
  score_threshold = 400,
  threshold_percentage = 20,
  export = FALSE,
  file_directory = NULL,
  export_format = "csv"
)

Arguments

genes_list	A list of gene IDs.
terms_list	A list of search terms.
rank_method	The method to rank pubmed results, either "weighted" or "total". Weighted ranks results based on order of terms inputted. Total ranks results on total sum of publications across all search term combinations. Defaults to "weighted".
species	The NCBI taxon ID of the species. Defaults to 9606 (Homo sapiens).
network_type	The type of string network to use, either "full" or "physical". Defaults to "full".
score_threshold	The minimum score threshold for string interactions. Defaults to 400.
threshold_percentage	Percentage threshold for ranking (default is 20%).
export	Logical indicating whether to export the results. Defaults to FALSE.
file_directory	Directory for saving the output files. Defaults to NULL.
export_format	Format for export, either "csv", "tsv", or "excel".

Value

A list containing the PubMed search results, STRING results, and summary results.

Examples

genes <- c("TP53", "BRCA1")
terms <- c("cancer", "tumor")
results <- descide(genes, terms, export = FALSE)
str(results)

DeSciDe documentation built on Sept. 1, 2025, 1:08 a.m.