Package {genefindr}

Title: Rapid Gene Characterization Using Public Genomic Databases
Version: 1.1.0
Description: A user-friendly interface for characterizing gene function by disease type and tissue site, integrating curated data from publicly available genomic and proteomic databases to support candidate gene prioritization in experimental workflows.
Depends: R (≥ 4.1.0)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 8.0.0
Imports: httr2, gtexr, ggplot2
URL: https://github.com/martincyd/genefindr
BugReports: https://github.com/martincyd/genefindr/issues
Suggests: knitr, rmarkdown, spelling, DESeq2, S4Vectors, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-08-01 18:22:26 UTC; cyd
Author: Cydnie Martin [aut, cre]
Maintainer: Cydnie Martin <martincydenise@gmail.com>
Repository: CRAN
Date/Publication: 2026-08-01 18:50:02 UTC

Characterize a gene using public genomic databases

Description

Characterize a gene using public genomic databases

Usage

findr(gene, disease = NULL, site = NULL)

Arguments

gene

Character. Gene symbol (e.g. "TP53")

disease

Character. Disease context (e.g. "alzheimer")

site

Character. Cancer site (e.g. "breast", "lung"). Can be a vector for multi-site comparison.

Value

Invisibly returns a data frame of results

Examples


findr("TP53", site = "breast")

Characterize top differentially expressed genes from a DESeq2 results object

Description

Characterize top differentially expressed genes from a DESeq2 results object

Usage

findr_from_deseq(
  deseq_results,
  site = NULL,
  disease = NULL,
  n_top = 20,
  padj_cutoff = 0.05,
  min_lfc = 1,
  direction = "both"
)

Arguments

deseq_results

A DESeqResults object from DESeq2::results()

site

Character. Cancer site (e.g. "breast", "lung")

disease

Character. Disease context for non-cancer queries

n_top

Integer. Number of top genes to characterize (default 20)

padj_cutoff

Numeric. Adjusted p-value cutoff (default 0.05)

min_lfc

Numeric. Minimum absolute log2 fold change (default 1.0)

direction

Character. "up", "down", or "both" (default "both")

Value

A data frame of gene characterization results

Examples


library(DESeq2)
fake_res <- data.frame(
  baseMean = c(100, 200, 150),
  log2FoldChange = c(2.5, -1.8, 3.1),
  lfcSE = c(0.3, 0.4, 0.3),
  stat = c(8.3, -4.5, 10.3),
  pvalue = c(0.0001, 0.001, 0.00001),
  padj = c(0.001, 0.01, 0.0001),
  row.names = c("TP53", "BRCA1", "EGFR")
)
fake_deseq <- DESeq2::DESeqResults(S4Vectors::DataFrame(fake_res))
findr_from_deseq(fake_deseq, site = "breast", n_top = 3)

Characterize multiple genes using public genomic databases

Description

Characterize multiple genes using public genomic databases

Usage

findr_multi(genes, disease = NULL, site = NULL, output = "print")

Arguments

genes

Character vector. Gene symbols (e.g. c("TP53", "BRCA1"))

disease

Character. Disease context

site

Character. Cancer site

output

Character. "print" or "table"

Value

Invisibly returns a data frame of results

Examples


findr_multi(c("TP53", "BRCA1"), site = "breast")

Plot gene association scores for multiple genes in a single disease context

Description

Plot gene association scores for multiple genes in a single disease context

Usage

findr_plot_genes(results, title = NULL)

Arguments

results

A data frame returned by findr_multi() with output = "table"

title

Optional plot title

Value

A ggplot2 object

Examples


results <- findr_multi(c("TP53", "BRCA1", "MYC"), site = "breast", output = "table")
findr_plot_genes(results)

Plot a heatmap of gene association scores across multiple cancer sites

Description

Plot a heatmap of gene association scores across multiple cancer sites

Usage

findr_plot_heatmap(results, title = NULL)

Arguments

results

A data frame returned by findr_multi() with output = "table"

title

Optional plot title

Value

A ggplot2 object

Examples

if (interactive()) {
  results <- findr_multi(c("TP53", "BRCA1", "EGFR"),
                         site = c("breast", "lung", "colon"),
                         output = "table")
  findr_plot_heatmap(results)
}

Plot association scores for a single gene across multiple disease sites

Description

Plot association scores for a single gene across multiple disease sites

Usage

findr_plot_sites(results, title = NULL)

Arguments

results

A data frame returned by findr_multi() with output = "table"

title

Optional plot title

Value

A ggplot2 object

Examples

if (interactive()) {
  results <- findr_sites_table("TP53", sites = c("breast", "lung"))
  findr_plot_sites(results)
}

Get gene characterization data across multiple cancer sites as a table

Description

Get gene characterization data across multiple cancer sites as a table

Usage

findr_sites_table(gene, sites)

Arguments

gene

Character. Gene symbol (e.g. "TP53")

sites

Character vector of cancer sites (e.g. c("breast", "lung", "colon"))

Value

A data frame with results for each site

Examples


results <- findr_sites_table("TP53", sites = c("breast", "lung"))
findr_plot_sites(results)