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pgxRpi

This is the development version of pgxRpi; to use it, please install the devel version of Bioconductor.

R wrapper for Progenetix


Bioconductor version: Development (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 uzh.ch>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("pgxRpi")

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

Documentation

Reference Manual PDF

Details

biocViews CopyNumberVariation, DataImport, GenomicVariation, Software
Version 0.99.14
In Bioconductor since BioC 3.19 (R-4.4)
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
System Requirements
URL https://github.com/progenetix/pgxRpi
Bug Reports https://github.com/progenetix/pgxRpi/issues
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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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/pgxRpi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pgxRpi
Package Short Url https://bioconductor.org/packages/pgxRpi/
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