Package: HPAanalyze 1.31.2

Anh Nhat Tran

HPAanalyze: Retrieve and analyze data from the Human Protein Atlas

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.

Authors:Anh Nhat Tran [aut, cre]

HPAanalyze_1.31.2.tar.gz
HPAanalyze_1.31.2.zip(r-4.7-any)HPAanalyze_1.31.2.zip(r-4.6-any)HPAanalyze_1.31.2.zip(r-4.5-any)
HPAanalyze_1.31.2.tgz(r-4.6-any)HPAanalyze_1.31.2.tgz(r-4.5-any)
HPAanalyze_1.31.2.tar.gz(r-4.7-any)HPAanalyze_1.31.2.tar.gz(r-4.6-any)
HPAanalyze_1.31.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HPAanalyze/json (API)

# Install 'HPAanalyze' in R:
install.packages('HPAanalyze', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/anhtr/hpaanalyze/issues

Datasets:

On BioConductor:HPAanalyze-1.31.2(bioc 3.24)HPAanalyze-1.30.0(bioc 3.23)

proteomicscellbiologyvisualizationsoftware

8.15 score 39 stars 50 scripts 534 downloads 1 mentions 16 exports 31 dependencies

Last updated from:cfad11eeb6. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING204
linux-develNOTE252
source / vignettesOK278
linux-releaseNOTE281
macos-releaseNOTE212
macos-oldrelNOTE212
windows-develNOTE157
windows-releaseNOTE145
windows-oldrelNOTE127
wasm-releaseOK118

Exports:hpaDownloadhpaExporthpaListParamhpaSearchhpaSubsethpaVishpaVisPathohpaVisSubcellhpaVisTissuehpaXmlhpaXmlAntibodyhpaXmlGethpaXmlParsehpaXmlProtClasshpaXmlTissueExprhpaXmlTissueExprSum

Dependencies:clicpp11dplyrfarvergenericsggplot2gluegridExtragtableisobandlabelinglifecyclemagrittropenxlsxpillarpkgconfigR6RColorBrewerRcpprlangS7scalesstringitibbletidyselectutf8vctrsviridisLitewithrxml2zip

Quick-start guide: Acquire and visualize the Human Protein Atlas (HPA) data in one function with HPAanalyze
Background | The different HPA data formats | HPAanalyze overview | Visualize protein expression data | Search HPA for genes of interest | Acquiring individual sample data from the Human Protein Atlas | Copyright
Rendered froma_HPAanalyze_quick_start.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2019-11-08

In-depth: Working with Human Protein Atlas (HPA) data in R with HPAanalyze
Summary | Background | The different HPA data formats | HPAanalyze overview | Obtaining HPAanalyze | Full dataset import, subsetting and export | Download and import data with hpaDownload() | The "histology" datasets | Other datasets | List available parameter for subsetting with hpaListParam() | Subset data with hpaSubset() | Export data with hpaExport() | Visualization | Unbrella function hpaVis() | Visualize tissue data with hpaVisTissue() | Visualize expression in cancer with hpaVisPatho() | Visualize subcellular location data with hpaVisSubcell() | Individual xml import and image downloading | The umbrella function hpaXml | Import xml file with hpaXmlGet() | View protein classes with hpaXmlProtClass() | Get summary and images of tissue expression with hpaXmlTissueExprSum() | Get details of individual IHC samples with hpaXmlAntibody() and hpaXmlTissueExpr() | Parse everything with hpaXmlParse() | Searching HPA data | Compatibility with hpar Bioconductor package | Acknowledgements | Copyright
Rendered fromb_HPAanalyze_indepth.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2019-11-08

Tutorial: Search the Human Protein Atlas from R with hpaSearch()
The case | The solution | A simple gene search | Exact matches | Choosing result columns | Advanced field queries | Feeding results straight into the rest of HPAanalyze | Copyright
Rendered fromh_HPAanalyze_case_search.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2026-08-05

Tutorial: Working with Human Protein Atlas (HPA) xml files offline
The case | The solution | Download and keep a local version of the xml files for yourself | Business as usual with hpaXml functions | Save your parsed objects | Copyright
Rendered fromd_HPAanalyze_case_offline_xml.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2019-11-08

Tutorial: Parse an entire HPA xml file into relational tibbles with hpaXmlParse()
The case | The solution | Import an xml file as usual | Parse everything with hpaXmlParse() | How the tables relate to each other | Worked example: joining tables together | Why this shape, and what to expect across genes | Save your parsed objects | Copyright
Rendered fromg_HPAanalyze_case_relational_xml.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2026-08-05

Tutorial: Combine HPAanalyze with your Human Protein Atlas (HPA) queries
The case | The solution | Create your query | Visualization | XML extraction | Copyright
Rendered fromc_HPAanalyze_case_query.Rmdusingknitr::rmarkdown

Last update: 2026-08-02
Started: 2019-11-08

Tutorial: Export Human Protein Atlas (HPA) data as JSON
The case | The solution | Download and subset data | Convert dataframes to JSON | Write JSON file | In one function | Copyright
Rendered frome_HPAanalyze_case_json.Rmdusingknitr::rmarkdown

Last update: 2026-08-02
Started: 2019-11-08

Tutorial: Download histology images from the Human Protein Atlas
The case | The solution | Get the download links | Download the images | Notes | Copyright
Rendered fromf_HPAanalyze_case_images.Rmdusingknitr::rmarkdown

Last update: 2026-08-02
Started: 2019-11-08

Code for figures from HPAanalyze paper
Figure 2 | Figure 3 | Figure 4 | Figure 5 | Copyright
Rendered fromz_HPAanalyze_paper_figures.Rmdusingknitr::rmarkdown

Last update: 2026-08-02
Started: 2019-11-08