gemma.R: gemma.R package: Access curated gene expression data and...

In PavlidisLab/Gemma-API: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

gemma.R package: Access curated gene expression data and differential expression analyses

Description

This package contains wrappers and convenience functions for Gemma's RESTful API that enables access to curated expression and differential expression data from over 15,000 published studies (as of mid-2022). Gemma (https://gemma.msl.ubc.ca) is a web site, database and a set of tools for the meta-analysis, re-use and sharing of transcriptomics data, currently primarily targeted at the analysis of gene expression profiles.

Details

Most users will want to start with the high-level functions like get_dataset_object, get_differential_expression_values and get_platform_annotations Additional lower-level methods are available that directly map to the Gemma RESTful API methods.

For more information and detailed usage instructions check the README, the function reference and the vignette.

All software-related questions should be posted to the Bioconductor Support Site: https://support.bioconductor.org

Author(s)

Javier Castillo-Arnemann, Jordan Sicherman, Ogan Mancarci, Guillaume Poirier-Morency

References

Lim, N. et al., Curation of over 10 000 transcriptomic studies to enable data reuse, Database, 2021. https://doi.org/10.1093/database/baab006

See Also

Useful links:

• https://pavlidislab.github.io/gemma.R/

• https://github.com/PavlidisLab/gemma.R

• Report bugs at https://github.com/PavlidisLab/gemma.R/issues

PavlidisLab/Gemma-API documentation built on Oct. 25, 2024, 10:25 a.m.