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R wrapper for Progenetix

Bioconductor version: Release (3.19)

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

Author: Hangjia Zhao [aut, cre] , Michael Baudis [aut]

Maintainer: Hangjia Zhao <hangjia.zhao at>

Citation (from within R, enter citation("pgxRpi")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction_1_loadmetadata HTML R Script
Introduction_2_loadvariants HTML R Script
Introduction_3_loadfrequency HTML R Script
Introduction_4_process_pgxseg HTML R Script
Reference Manual PDF


biocViews CopyNumberVariation, DataImport, GenomicVariation, Software
Version 1.0.3
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2)
Imports utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, plyr, GenomicRanges, SummarizedExperiment, S4Vectors, parallelly
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Suggests BiocStyle, rmarkdown, knitr, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pgxRpi_1.0.3.tar.gz
Windows Binary
macOS Binary (x86_64) pgxRpi_1.0.3.tgz
macOS Binary (arm64) pgxRpi_1.0.3.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
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Old Source Packages for BioC 3.19 Source Archive