HPAanalyze

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see HPAanalyze.

Retrieve and analyze data from the Human Protein Atlas

Bioconductor version: 3.21

Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data. HPAanalyze is designed to fullfill 3 main tasks: (1) Import, subsetting and export downloadable datasets; (2) Visualization of downloadable datasets for exploratory analysis; and (3) Working with the individual XML files. This package aims to serve researchers with little programming experience, but also allow power users to use the imported data as desired.

Author: Anh Nhat Tran [aut, cre]

Maintainer: Anh Nhat Tran <trannhatanh89 at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("HPAanalyze")

1. Quick-start guide: Acquire and visualize the Human Protein Atlas (HPA) data in one function with HPAanalyze HTML R Script

2. In-depth: Working with Human Protein Atlas (HPA) data in R with HPAanalyze HTML R Script

3. Tutorial: Combine HPAanalyze with your Human Protein Atlas (HPA) queries HTML R Script

4. Tutorial: Working with Human Protein Atlas (HPA) xml files offline HTML R Script

5. Tutorial: Export Human Protein Atlas (HPA) data as JSON HTML R Script

6. Tutorial: Download histology images from the Human Protein Atlas HTML R Script

99. Code for figures from HPAanalyze paper HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBiology, Proteomics, Software, Visualization

Version 1.26.1

In Bioconductor since BioC 3.8 (R-3.5) (7 years)

License GPL-3 + file LICENSE

Depends R (>= 3.5.0)

Imports dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra

System Requirements

URL https://github.com/anhtr/HPAanalyze https://anhtr.github.io/HPAanalyze/

Bug Reports https://github.com/anhtr/HPAanalyze/issues

Suggests knitr, rmarkdown, markdown, devtools, BiocStyle

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package HPAanalyze_1.26.1.tar.gz

Windows Binary (x86_64) HPAanalyze_1.26.1.zip (64-bit only)

macOS Binary (x86_64) HPAanalyze_1.26.1.tgz

macOS Binary (arm64) HPAanalyze_1.26.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/HPAanalyze

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HPAanalyze

Bioc Package Browser https://code.bioconductor.org/browse/HPAanalyze/

Package Short Url https://bioconductor.org/packages/HPAanalyze/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.21 Source Archive