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

peter.suber's bookmarks 2019-03-17

Summary:

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.

Link:

https://peerj.com/articles/6509/

From feeds:

Open Access Tracking Project (OATP) » peter.suber's bookmarks

Tags:

oa.new oa.data oa.biology oa.floss oa.medicine oa.tools

Date tagged:

03/17/2019, 10:41

Date published:

03/17/2019, 06:41