https://github.com/ajank/Romulus

Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data
https://github.com/ajank/Romulus

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

• Host: GitHub
• URL: https://github.com/ajank/Romulus
• Owner: ajank
• Created: 2014-10-09T15:10:46.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2019-03-06T14:01:12.000Z (over 5 years ago)
• Last Synced: 2024-02-12T23:47:41.654Z (5 months ago)
• Language: R
• Homepage:
• Size: 229 KB
• Stars: 9
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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• awesome-atac-analysis - Romulus

README

        
### 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:

```R

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:

```R

library(devtools)

install_github("ajank/Romulus")

```

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

```R

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.