Package: molpathR 0.1.0.9001

R. Heller

molpathR: Molecular Pathology Data Platform for Clinical NGS Integration

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.

Authors:R. Heller [aut, cre]

molpathR_0.1.0.9001.tar.gz
molpathR_0.1.0.9001.zip(r-4.7-any)molpathR_0.1.0.9001.zip(r-4.6-any)molpathR_0.1.0.9001.zip(r-4.5-any)
molpathR_0.1.0.9001.tgz(r-4.6-any)molpathR_0.1.0.9001.tgz(r-4.5-any)
molpathR_0.1.0.9001.tar.gz(r-4.7-any)molpathR_0.1.0.9001.tar.gz(r-4.6-any)
molpathR_0.1.0.9001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
molpathR/json (API)

# Install 'molpathR' in R:
install.packages('molpathR', repos = c('https://cttir.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cttir/molpathr/issues

Pkgdown/docs site:https://cttir.github.io

On CRAN:

Conda:

bioinformaticsclinical-genomicsggplot2molecular-pathologymolpathngsoncologyshinyvariant-analysis

4.48 score 15 scripts 33 exports 90 dependencies

Last updated from:133e5ecc53. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK240
source / vignettesOK313
linux-releaseOK252
macos-releaseOK202
macos-oldrelOK129
windows-develOK189
windows-releaseOK193
windows-oldrelOK189
wasm-releaseOK151

Exports:mp_add_datamp_build_dbmp_example_dbmp_example_filesmp_get_patientmp_load_dbmp_merge_dbmp_plot_cohort_overviewmp_plot_mutation_spectrummp_plot_survivalmp_plot_timelinemp_plot_vaf_distributionmp_plot_variant_landscapemp_query_patientsmp_query_samplesmp_query_variantsmp_read_automp_read_bammp_read_fastqmp_read_nexus_clinicalmp_read_nexus_pathologymp_read_pdf_reportmp_read_survivalmp_read_vcfmp_read_xml_reportmp_run_appmp_save_dbmp_searchmp_summarymp_validate_dbnew_molpath_dbnew_molpath_parsedvalidate_molpath_db

Dependencies:askpassbase64encbitbit64bslibcachemcellrangerclicliprcommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeopensslotelpdftoolspillarpkgconfigplotlyprettyunitsprogresspromisespurrrqpdfR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownS7sassscalesshinyshinyWidgetssourcetoolsstringistringrsurvivalsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxml2xtableyaml

Data Import Guide
Scope | A runnable import | VCF calls and missing annotations | Reports and raw sequencing | Validation, merging and persistence
Rendered fromdata-import.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-05-04

Getting Started with molpathR
Installation | Quick start | Explore the data | Query patients | Query variants | Visualize | Launch the Shiny app
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-05-04

Interactive Shiny Application
Launching the app | Application tabs | Tab 1: Database | Tab 2: Patients | Tab 3: Variants | Tab 4: Reports | Tab 5: Survival | Tab 6: Export | Cross-tab interactivity | Deployment
Rendered fromshiny-app.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-05-04

Visualization Guide
Overview | Variant landscape | VAF distribution | Survival analysis | Cohort overview | Patient timeline | Customization
Rendered fromvisualization.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-05-04

Readme and manuals

Help Manual

Help pageTopics
Add parsed data to an existing molpath_dbmp_add_data
Build a molpath_db from parsed data objectsmp_build_db
Create a synthetic molecular pathology databasemp_example_db
Write synthetic example files to a directorymp_example_files
Get all data for a single patientmp_get_patient
Load a molpath_db from diskmp_load_db
Merge two molpath_db objectsmp_merge_db
Plot cohort overviewmp_plot_cohort_overview
Plot mutation spectrummp_plot_mutation_spectrum
Plot Kaplan-Meier survival curvesmp_plot_survival
Plot patient timelinemp_plot_timeline
Plot variant allele frequency distributionmp_plot_vaf_distribution
Plot variant landscape (oncoplot)mp_plot_variant_landscape
Filter patients in a molpath_dbmp_query_patients
Filter samples in a molpath_dbmp_query_samples
Filter variants in a molpath_dbmp_query_variants
Automatically read a molecular pathology filemp_read_auto
Read a BAM filemp_read_bam
Read a FASTQ filemp_read_fastq
Read Nexus clinical datamp_read_nexus_clinical
Read Nexus pathology datamp_read_nexus_pathology
Read a PDF pathology reportmp_read_pdf_report
Read survival / outcome datamp_read_survival
Read a VCF filemp_read_vcf
Read an XML variant reportmp_read_xml_report
Launch the molpathR Shiny applicationmp_run_app
Save a molpath_db to diskmp_save_db
Free-text search across a molpath_dbmp_search
Cohort-level summary of a molpath_dbmp_summary
Validate a molpath_db for referential integrity and completenessmp_validate_db
Create a new molpath_db objectnew_molpath_db
Create a new molpath_parsed objectnew_molpath_parsed
Print a molpath_db objectprint.molpath_db
Print a molpath_parsed objectprint.molpath_parsed
Summarise a molpath_db objectsummary.molpath_db
Summarise a molpath_parsed objectsummary.molpath_parsed
Validate a molpath_db objectvalidate_molpath_db