pgxRpi
This is the released version of pgxRpi; for the devel version, see pgxRpi.
R wrapper for Progenetix
Bioconductor version: Release (3.23)
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("pgxRpi")):Hangjia Zhao, Michael Baudis. pgxRpi: R wrapper for Progenetix. doi:10.18129/B9.bioc.pgxRpi, R package version 1.7.0, 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")
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_load_metadata | HTML | R Script |
| Introduction_2_query_variants | HTML | R Script |
| Introduction_3_access_cnv_frequency | HTML | R Script |
| Introduction_4_process_pgxseg | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, DataImport, GenomicVariation, Software |
| Version | 1.7.0 |
| 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 |
See More
| 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 | pgxRpi_1.7.0.tar.gz |
| Windows Binary (x86_64) | pgxRpi_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | pgxRpi_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | pgxRpi_1.7.0.tgz |
| 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 |