pgxRpi

This is the development version of pgxRpi; for the stable release version, see pgxRpi.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

R wrapper for Progenetix

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-8376-5751 , Michael Baudis [aut] ORCID: 0000-0002-9903-4248

Maintainer: Hangjia Zhao <hangjia.zhao at uzh.ch>

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

Hangjia Zhao, Michael Baudis. pgxRpi: R wrapper for Progenetix. doi:10.18129/B9.bioc.pgxRpi, R package version 1.9.0, https://bioconductor.org/packages/pgxRpi.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("pgxRpi")

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

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DataImport, GenomicVariation, Software
Version	1.9.0
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply
System Requirements
URL	https://github.com/progenetix/pgxRpi
Bug Reports	https://github.com/progenetix/pgxRpi/issues

Suggests	BiocStyle, rmarkdown, knitr, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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/
Package Downloads Report	Download Stats