Comp-04. R Tools for Exploratory Analysis of Publicly Available Data: Hpaanalyze and Beyond
Year: 2018
Type: conference-abstract
Abstract: The Human Protein Atlas (HPA) is a comprehensive resource for exploration of human proteome which contains a vast amount of proteomics and transcriptomics data generated from antibody-based tissue micro-array profiling and RNA deep-sequencing. Data from the HPA are freely available via proteinatlas.org, allowing scientists to access and incorporate the data into their research. Previously, the R package hpar has been created for fast and easy programmatic access of HPA data. Here, we introduce HPAanalyze, an R package aims to simplify exploratory data analysis from those data, as well as provide other complementary functionality to hpar. HPAanalyze is an R package for retrieving and performing exploratory data analysis from HPA. It provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as download all staining images of interest. The package is free, open source, and available via Github. CONCLUSIONS: HPAanalyze intergrates into the R workflow via the tidyverse philosophy and data structures, and can be used in combination with Bioconductor packages for easy analysis of HPA data.
Source: Neuro-Oncology
Authors: Anh Tran, Anita Hjelmeland
Institution: University of Alabama at Birmingham
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
OpenAlex ID: W2900102150