pgxRpi
This is the development version of pgxRpi; for the stable release version, see pgxRpi.
R wrapper for Progenetix
Bioconductor version: Development (3.21)
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:
Maintainer: Hangjia Zhao <hangjia.zhao at uzh.ch>
citation("pgxRpi")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, DataImport, GenomicVariation, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pgxRpi_1.3.0.tar.gz |
| Windows Binary (x86_64) | pgxRpi_1.3.0.zip (64-bit only) |
| macOS Binary (x86_64) | pgxRpi_1.3.0.tgz |
| macOS Binary (arm64) | pgxRpi_1.3.0.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 |