RTFBS: Transcription Factor Binding Sites... in R

Introduction

RTFBS is an R software package used to identify transcription factor binding sites. It contains functions for data pre-processing, site identification & scoring, FDR calculation, and score/FDR thresholding. RTFBS provides a variety of options, allowing users flexibility, all within a highly-developed statistical programming environment.

Download

Package source: rtfbs_0.3.3.tar.gz
Windows binary:rtfbs_0.3.3.zip
Development version:rtfbs_0.3.3.tar.gz
Latest Windows build (devel):rtfbs_0.3.3.zip

Install

RTFBS should install like any R package. It can be obtained and installed via CRAN from within R using the command:
> install.packages("rtfbs")

Note that if you are running Windows or Mac OS X, you will need an up-to-date version of R for this command to work. On Mac OS X with xcode, you can install onto an older R version with the command:
> install.packages("rtfbs", type="source")

Or to use the package files provided on this page, use one of these (depending on your platform):
> install.packages("rtfbs_0.3.3.tar.gz", repos=NULL) #(to install from source code)
> install.packages("rtfbs_0.3.3.zip", repos=NULL) #(to install windows binary)

The package source can also be installed from the command line on non-Windows platforms using the command:
R CMD INSTALL rtfbs_0.3.3.tar.gz

NOTE: If you do not have administrator privileges, you may need to specify a directory where the package will be stored. This can be done with the "library" argument to install.packages, or by using R CMD INSTALL --library=/path/to/library on the command line.

Documentation

PDFSweave sourcedescription
vignette.pdfvignette.RnwRead in sequence data & PWM, data pre-processing, site identification & scoring, FDR thresholding of identified sites
rtfbs-manual.pdf Reference manual

Plans

Our next step for RTFBS is to add user supported scoring functions.


Contact

Problems, questions, feature requests should be directed to rtfbs-help-l@cornell.edu.