HPAanalyze
This is the released version of HPAanalyze; for the devel version, see HPAanalyze.
Retrieve and analyze data from the Human Protein Atlas
Bioconductor version: Release (3.23)
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("HPAanalyze")):Anh Nhat Tran. HPAanalyze: Retrieve and analyze data from the Human Protein Atlas. doi:10.18129/B9.bioc.HPAanalyze, R package version 1.30.0, https://bioconductor.org/packages/HPAanalyze.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBiology, Proteomics, Software, Visualization |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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 |
| Bug Reports | https://github.com/anhtr/HPAanalyze/issues |
See More
| Suggests | knitr, rmarkdown, devtools, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HPAanalyze_1.30.0.tar.gz |
| Windows Binary (x86_64) | HPAanalyze_1.30.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HPAanalyze_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | HPAanalyze_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HPAanalyze |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HPAanalyze |
| Package Short Url | https://bioconductor.org/packages/HPAanalyze/ |
| Package Downloads Report | Download Stats |