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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

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

browseVignettes("pgxRpi")
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
NEWS Text

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
See More
Suggests BiocStyle, rmarkdown, knitr, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package pgxRpi_0.99.14.tar.gz
Windows Binary pgxRpi_0.99.14.zip
macOS Binary (x86_64) pgxRpi_0.99.14.tgz
macOS Binary (arm64) pgxRpi_0.99.14.tgz
Source Repository git clone https://git.bioconductor.org/packages/pgxRpi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pgxRpi
Bioc Package Browser https://code.bioconductor.org/browse/pgxRpi/
Package Short Url https://bioconductor.org/packages/pgxRpi/
Package Downloads Report Download Stats