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HPAStainR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see HPAStainR.

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


Bioconductor version: Release (3.18)

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>

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

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

Reference Manual PDF

Details

biocViews GeneExpression, GeneSetEnrichment, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.1.0), dplyr, tidyr
Imports utils, stats, scales, stringr, tibble, shiny, data.table
System Requirements 4GB of RAM
URL
Bug Reports https://github.com/tnieuwe/HPAstainR
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Suggests knitr, BiocManager, qpdf, hpar, testthat, rmarkdown
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Package Archives

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

Source Package
Windows Binary
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
Package Short Url https://bioconductor.org/packages/HPAStainR/
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