https://github.com/mahshaaban/cregulomedb

Build the database file for cRegulome package
https://github.com/mahshaaban/cregulomedb

cancer-genomics databases datascience microrna r tcga-data transcription-factors

Last synced: about 2 months ago
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Build the database file for cRegulome package

• Host: GitHub
• URL: https://github.com/mahshaaban/cregulomedb
• Owner: MahShaaban
• Created: 2017-08-08T11:59:56.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2018-09-20T05:29:02.000Z (over 6 years ago)
• Last Synced: 2023-08-03T15:25:10.867Z (over 1 year ago)
• Topics: cancer-genomics, databases, datascience, microrna, r, tcga-data, transcription-factors
• Language: R
• Size: 20.5 KB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# 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](http://cistrome.org/CistromeCancer/).

This data is based on integrative analysis of public tarnscription factor ChIP-seq data and The Cancer Genome Atlas

[(TCGA)](https://tcga-data.nci.nih.gov) data. The microRNA correlation data are obtained from [miRCancerdb](https://mahshaaban.shinyapps.io/miRCancerdb/) 

database. [miRCancerdb](https://mahshaaban.shinyapps.io/miRCancerdb/) is based on a similar analysis using [(TCGA)](https://tcga-data.nci.nih.gov)

data and [TargetScan](http://www.targetscan.org) 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`](https://github.com/MahShaaban/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](https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/9537385/cRegulome.db.gz).

## More    

+ For more about the cRegulome R package, [here](https://github.com/MahShaaban/cRegulome).  

+ For Citations, [here]().