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Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data

Romulus is a computational method to accurately identify individual transcription factor binding sites from genome sequence information and cell-type--specific experimental data, such as DNase-seq. It combines the strengths of its predecessors, CENTIPEDE and Wellington, while keeping the number of free parameters in the model robustly low. The method is unique in allowing for multiple binding states for a single transcription factor, differing in their cut profile and overall number of DNase I cuts.

Documentation

A PDF version of the Romulus package manual is available from http://www.mimuw.edu.pl/~ajank/Romulus/Romulus-manual.pdf.

Installation

The most recent stable version of Romulus is available from http://www.mimuw.edu.pl/~ajank/Romulus/Romulus_1.0.3.tar.gz. Please install it using the following R command:

install.packages("Romulus_1.0.3.tar.gz", repos = NULL, type = "source")

Alternatively, the development version can be installed directly from GitHub with the following two R commands:

library(devtools)
install_github("ajank/Romulus")

If you do not have the package `devtools´ installed, please install it first:

install.packages("devtools")

Citation

Please cite Romulus as:

Jankowski, A., Tiuryn, J. and Prabhakar, S. (2016). Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data. Bioinformatics 32, 2419-2426. doi: 10.1093/bioinformatics/btw209.