Postdoc - Biomedicine

cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer.


Journal article


Mahmoud Ahmed, Deok Ryong Kim
PeerJ, vol. 7, 2019, pp. e6509


View PDF PubMed
Cite

Cite

APA
Ahmed, M., & Kim, D. R. (2019). cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer. PeerJ, 7, e6509.

Chicago/Turabian
Ahmed, Mahmoud, and Deok Ryong Kim. “CRegulome: an R Package for Accessing MicroRNA and Transcription Factor-Gene Expression Correlations in Cancer.” PeerJ 7 (2019): e6509.

MLA
Ahmed, Mahmoud, and Deok Ryong Kim. “CRegulome: an R Package for Accessing MicroRNA and Transcription Factor-Gene Expression Correlations in Cancer.” PeerJ, vol. 7, 2019, p. e6509.


Abstract

Background: Transcription factors and microRNAs play a critical role in regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factor and microRNA targets and their role in the development of diseases including cancers. The availability of public access high-throughput data allows researchers to make data-driven predictions.
Implementation: Here, we developed an R package called cRegulome to access, manage and visualize data from open source databases. The package provides a programmatic access to the regulome (transcription factor and microRNA) expression correlations with target genes of different cancer types. It obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to query, interact with and visualize the correlation data.
Availability: cRegulome is available on the comprehensive R archive network (CRAN) and the source code is hosted on GitHub as part of the ROpenSci on-boarding collection, https://github.com/ropensci/cRegulome.