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Build the database file for cRegulome package
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README.md

cRegulomedb

Overview

The scripts in this repository are used to build and update the database file used with the R pacakge cRegulome. cRegulome is R language interface to access pre-caculated expression correlation of regulome (transcription factors & microRNA) and genes in cancers.

Data sources

The transcription factors correlation data are obtained from Cistrome Cancer. This data is based on integrative analysis of public tarnscription factor ChIP-seq data and The Cancer Genome Atlas (TCGA) data. The microRNA correlation data are obtained from miRCancerdb database. miRCancerdb is based on a similar analysis using (TCGA) data and TargetScan annotations.

Build/update the database file

This repository contains two R scripts; build_tf.R and build_mir.R and a simple makefile. By running make in the a UNIX shell, the build scripts load the required libraries and including sqlome that includes the nessecary funcions to build the database. To do that locally:

git clone https://github.com/MahShaaban/cRegulomedb
cd cRegulomedb
make

Pre-built copy

A pre-built copy of the database file can be obtained from here.

More

  • For more about the cRegulome R package, here.
  • For Citations, here.
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