curatedPCaData

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

Curated Prostate Cancer Data

Bioconductor version: Development (3.21)

The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in.

Author: Teemu Daniel Laajala [aut, cre] (ORCID: ), Jordan Creed [ctb], Christelle Colin Leitzinger [ctb], Varsha Sreekanth [ctb], Federico Calboli [ctb], Kalaimathy Singaravelu [ctb], Michael Orman [ctb], Alex Soupir [ctb], Anni Halkola [ctb]

Maintainer: Teemu Daniel Laajala <teelaa at utu.fi>

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

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("curatedPCaData")

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("curatedPCaData")

Overview to curatedPCaData	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CancerData, CopyNumberVariationData, ExperimentData, ExperimentHub, ExpressionData, GEO, Homo_sapiens_Data, MicroarrayData, ProstateCancerData, RNASeqData, ReproducibleResearch, Somatic
Version	1.3.0
License	CC BY 4.0
Depends	R (>= 4.4.0), S4Vectors(>= 0.23.18), MultiAssayExperiment, RaggedExperiment
Imports	ExperimentHub, AnnotationHub, utils, methods, rlang, stats, reshape2
System Requirements
URL	https://github.com/Syksy/curatedPCaData
Bug Reports	https://github.com/Syksy/curatedPCaData/issues

Suggests	BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer, ComplexHeatmap, corrplot, formatR
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	curatedPCaData_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/curatedPCaData
Source Repository (Developer Access)	git clone [email protected]:packages/curatedPCaData
Package Short Url	https://bioconductor.org/packages/curatedPCaData/
Package Downloads Report	Download Stats