Package: molpathR
Title: Molecular Pathology Data Platform for Clinical NGS Integration
Description: A unified platform for ingesting, linking, querying, and
        visualizing molecular pathology data from heterogeneous sources
        including NGS files (FASTQ, BAM, VCF), XML variant
        interpretation reports, structured pathology PDF reports,
        pathology and clinical information systems, and survival
        outcome data. Provides a searchable in-memory database and an
        interactive Shiny application for clinical exploration and
        cohort analysis. Raw sequence and alignment readers do not
        perform variant calling or clinical interpretation.
Version: 0.1.0.9001
Authors@R: person("R.", "Heller", email = "raban.heller@charite.de",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8006-9742"))
License: MIT + file LICENSE
URL: https://github.com/cttir/molpathR,
        https://cttir.github.io/molpathR/
BugReports: https://github.com/cttir/molpathR/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.1.0)
Imports: tibble, dplyr, tidyr, readr, readxl, xml2, jsonlite, pdftools,
        stringr, rlang, cli, ggplot2, survival, DT, shiny (>= 1.6.0),
        bslib (>= 0.5.0), plotly, shinyWidgets, stats, utils, tools,
        methods
Suggests: Rsamtools, VariantAnnotation, GenomicRanges, ShortRead,
        Biostrings, BiocGenerics, IRanges, SummarizedExperiment,
        testthat (>= 3.0.0), knitr, rmarkdown, pkgdown, withr,
        shinytest2, writexl
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/Needs/website: CTTIR/themakR
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev libjpeg-dev libuv1-dev
        libxml2-dev libssl-dev libpoppler-cpp-dev poppler-data
        libx11-dev zlib1g-dev
Repository: https://cttir.r-universe.dev
Date/Publication: 2026-11-03 11:54:04 UTC
RemoteUrl: https://github.com/CTTIR/molpathR
RemoteRef: HEAD
RemoteSha: 133e5ecc539f3ca84e84274bbed615228c6f9d6f
NeedsCompilation: no
Packaged: 2026-11-03 18:14:57 UTC; root
Author: R. Heller [aut, cre] (ORCID: <https://orcid.org/0000-0001-8006-9742>)
Maintainer: R. Heller <raban.heller@charite.de>