molpathR

molpathR is a unified molecular pathology data platform that ingests heterogeneous clinical and genomic data sources (VCF, BAM, FASTQ, XML reports, PDF reports, clinical information systems, survival data), builds a queryable in-memory database, and provides an interactive Shiny application for clinical exploration and visualization.

Installation

Install the development version from GitHub:

# install.packages("remotes")
remotes::install_github("r-heller/molpathR")

Quick example

library(molpathR)

# Load example database with synthetic data
db <- mp_example_db(n_patients = 50, seed = 42)
db

# Query pathogenic TP53 variants
tp53 <- mp_query_variants(db, genes = "TP53", classification = "Pathogenic")
head(tp53[, c("sample_id", "gene", "variant", "classification", "vaf")])

# Survival analysis by diagnosis
mp_plot_survival(db, group_by = "diagnosis", type = "os")

Launch the Shiny app

mp_run_app(db)

Features

• Parsers for VCF, FASTQ, BAM, XML reports, PDF reports, clinical systems, and survival data
• Relational in-memory database linking patients, samples, variants, reports, clinical, and survival data
• Query engine with tidy evaluation and free-text search
• Publication-ready plots: variant landscapes, mutation spectra, survival curves, cohort overviews
• Interactive Shiny application with 6 tabs for clinical exploration

Documentation

• Getting Started
• Data Import Guide
• Visualization Guide
• Shiny Application

License

MIT License. See LICENSE.md for details.