HPAStainR

DOI: 10.18129/B9.bioc.HPAStainR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see HPAStainR.

Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes

Bioconductor version: 3.17

This package is built around the HPAStainR function. The purpose of the HPAStainR function is to query the visual staining data in the Human Protein Atlas to return a table of staining ranked cell types. The function also has multiple arguments to personalize to output as well to include cancer data, csv readable names, modify the confidence levels of the results and more. The other functions exist exclusively to easily acquire the data required to run HPAStainR.

Author: Tim O. Nieuwenhuis [aut, cre]

Maintainer: Tim O. Nieuwenhuis <tnieuwe1 at jhmi.edu>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("HPAStainR")

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("HPAStainR")

 

HTML	R Script	HPAStainR
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneSetEnrichment, Software
Version	1.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), dplyr, tidyr
Imports	utils, stats, scales, stringr, tibble, shiny, data.table
LinkingTo
Suggests	knitr, BiocManager, qpdf, hpar, testthat, rmarkdown
SystemRequirements	4GB of RAM
Enhances
URL
BugReports	https://github.com/tnieuwe/HPAstainR
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HPAStainR_1.9.0.tar.gz
Windows Binary	HPAStainR_1.9.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/HPAStainR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HPAStainR
Bioc Package Browser	https://code.bioconductor.org/browse/HPAStainR/
Package Short Url	https://bioconductor.org/packages/HPAStainR/
Package Downloads Report	Download Stats