target_ranking

Code for the BMC Genomics paper (Integrating binding and expression data to predict transcription factors combined function). The article describes the Bioconductor R package target

Setting up the docker environment

The analysis was run on a docker image based on the the latest rocker/verse. Other R packages were added to the image and were made available as an image that can be obtained and launched on any local machine running docker.

$ docker pull bcmslab/target:latest
$ docker run -it bcmslab/target:latest bash

Obtaining the source code

The source code is hosted publicly on this repository in a form of research compendium. This includes the scripts to reproduce the figures and tables in this manuscript. From within the container, git can be used to clone the source code.

The following code clones the repository containing the source code.

$ git clone http://github.com/BCMSLab/target_ranking

Generating figures and tables

The script to generate the figures and tables in the manuscirpt can be run through Makefile

$ cd target_ranking
$ make

Details of the R environment

The version of R that was used to perform this analysis is the 3.6.2 (2019-12-12) on x86\_64-pc-linux-gnu.