genefindr

Rapid gene characterization without leaving R.

genefindr is an R package that provides instant, comprehensive gene characterization by querying eight public databases simultaneously. Designed for researchers who need quick, reliable gene overviews to support experimental decisions — from western blot candidate selection to target prioritization.

Why genefindr?

Characterizing a gene typically means manually searching GeneCards, then Open Targets, then Human Protein Atlas, then PubMed… genefindr does all of this in one function call.

Installation

# Install from GitHub
pak::pak("martincyd/genefindr")

# Or install from local folder
pak::pak("local::path/to/genefindr")

Quick Start

library(genefindr)

# Single gene, single context
findr("TP53", site = "breast")

# Multiple genes
findr_multi(c("TP53", "BRCA1", "MYC"), site = "breast")

# Multi-site comparison
findr("TP53", site = c("breast", "lung", "colon"))

# Export results as a table
results <- findr_multi(c("TP53", "BRCA1"), site = "breast", output = "table")
write.csv(results, "candidates.csv")

# Non-cancer disease context
findr("APOE", disease = "alzheimer")

# Works with non-coding RNAs too
findr("MALAT1", site = "lung")

Example Output

============================
Gene: TP53
Context: breast
============================
Name: tumor protein p53
Type: protein-coding
Molecular weight: 43,653 Da
Subcellular location: Cytoplasm, Nucleus, PML body, Endoplasmic reticulum...
Isoforms: 9 (p53, p53gamma, Del40-p53, Del40-p53beta...)
Note: multiple isoforms detected — verify antibody targets correct isoform

PubMed publications: 38,434 total | 4,636 in context of breast

Summary: This gene encodes a tumor suppressor protein...

--- Disease Association (Open Targets) ---
Association score: 0.743
Matched disease: Hereditary breast cancer

--- Protein & Expression (Human Protein Atlas) ---
Protein evidence: Evidence at protein level
Antibody available: Yes

--- Normal Expression (GTEx) ---
Suggested positive control tissue: Skin Sun Exposed Lower leg (37 TPM)

--- Tumor Mutation Frequency (cBioPortal/TCGA) ---
Mutated in 32.6% of TCGA BREAST tumors (353/1084 samples, TCGA PanCancer Atlas 2018)

--- Clinical Variants (ClinVar) ---
Pathogenic: 1,734 | Benign: 1,962 | VUS: 2,252

============================
Data sources: MyGene.info, Open Targets, Human Protein Atlas, UniProt, GTEx, cBioPortal, PubMed, ClinVar
============================

Data Sources

Database	Data provided
MyGene.info	Gene name, type, summary
Open Targets	Disease association scores
Human Protein Atlas	Protein evidence, antibody availability
UniProt	Molecular weight, subcellular location, isoforms
GTEx	Normal tissue expression
cBioPortal/TCGA	Tumor mutation frequency
PubMed	Publication counts
ClinVar	Clinical variant counts

Supported Sites

breast, prostate, lung, colon, ovarian, liver, brain, pancreatic, skin, blood

Note on gene symbols

genefindr requires official HGNC gene symbols. Common aliases may return unexpected results:

Common name	Official symbol
HER2	ERBB2
p53	TP53
cMYC	MYC
VEGF	VEGFA
HER1	EGFR

When in doubt, look up the official symbol at genenames.org.

Functions

findr() — characterize a single gene
findr_multi() — characterize multiple genes at once

Citation

If you use genefindr in your research, please cite the data sources above and this package: Martin, Cydnie (2026). genefindr: Rapid Gene Characterization Using Public Genomic Databases. R package version 0.0.0.9000. https://github.com/martincyd/genefindr

License

GPL-3