Skip to content
/ gtexRNA Public

Gene expression retrieval with GTEx API

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md
Notifications You must be signed in to change notification settings

sigven/gtexRNA

Repository files navigation

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:

R-CMD-check

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.

About

Gene expression retrieval with GTEx API

Topics

Resources

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md

Code of conduct

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages