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TSSi package: Transcription Start Site Identification

Table of Contents

Summary

The TSSi package identifies and normalizes transcription start sites in high-throughput sequencing data.

Along with the advances in high-throughput sequencing, the detection of transcription start sites (TSS) using CAP-capture techniques has evolved recently. While many experimental applications exist, the analysis of such data is still non-trivial. Approaching this, the TSSi package offers a flexible statistical preprocessing for CAP-capture data and an automated identification of start sites.

Authors: Clemens Kreutz, Julian Gehring, Jens Timmer
Maintainer: Julian Gehring <julian.gehring (at) embl.de>

Availability, source code, and licensing

The TSSi package is written for R and part of the bioconductor project since the 2.9 release in November 2011. This provides the latest stable release version and the current developer version, including builts for major platforms supported by R.

The complete source code of the package is publically accessible at github and licenced under the General Public License version 3 (GPL-3). You are free to use the software for any purposes and you are also welcome to contribute to it in any way.

Usage

Installation

In order to install the latest stable version of the TSSi package from the bioconductor repository, simply run in your R session:

   source("http://bioconductor.org/biocLite.R")
   biocLite("TSSi")

Alternatively, you can also download the built packages from bioconductor and install them manually:

   install.packages("path/to/TSSi_x.y.z")

Please note that the first method is generally the best choice.

Loading the package

After the package has been installed, you can load it:

   library(TSSi)

Documentation

A comprehensive example session on how to analyze gene sets with the TSSi package can be found in the vignette of the package. This can also be assessed as a pdf file from the bioconductor website or within R:

   vignette("TSSi")

Detailed descriptions of the objects, functions, and their parameters are provided in the help pages. For details about individual parts, e.g. the segmentizeCounts method, you can read the help file within R:

   ?segmentizeCounts

Contact and contribution

If you have any questions, comments, or contributions:

Date: 2011-11-06 08:44:41 CET

Author: Julian Gehring