gtexRNA - Quick retrieval of tissue-specific expression data from GTEx

Overview

This R package provides a simple wrapper function to query GTEx (v8) for gene expression levels in healthy human tissues, using a set of human gene symbols and a particular tissue type as its main arguments. The function utilizes the GTEx API to retrieve the data. A brief example:

Example usage

devtools::install_github('sigven/gtexRNA')

exp_dist_gtex <- gtexRNA::get_tpm_data(genes = c('KRAS','BRAF'), tissue_type = 'Bladder')

exp_dist_gtex is a data.frame with all gene expression levels pr. sample, provided with TPM and log2(TPM + 1).

To see the available types of tissues that can be queried, explore the metadata file:

unique(gtexRNA::sampleMetadata$tissue_site_detail_id)

PS: We have not yet found a way to retrieve the actual sample identifiers from the API method, so get_tpm_data() will currently thus return sample records without any sample identifiers.

Contact

sigven@ifi.uio.no

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.