Bioconductor-mirror/TSRchitect: Promoter identification from large-scale TSS profiling data
Version 1.1.0

In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in eukaryotes. Techniques that identify the 5' end of mRNAs, most notably CAGE, have mapped the promoter landscape across a number of model organisms. Due to the variability of TSS distributions and the transcriptional noise present in datasets, precisely identifying the active promoter(s) for genes from these datasets is not straightforward. TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT). Along with the coordiantes of identified TSRs, TSRchitect also calculates the width, abundance and Shape Index, and handles biological replicates for expression profiling. Finally, TSRchitect imports annotation files, allowing the user to associate identified promoters with genes and other genomic features. Three detailed examples of TSRchitect's utility are provided in the User's Guide, included with this package.

Getting started

Package details

AuthorR. Taylor Raborn [aut, cre, cph] Volker P. Brendel [aut, cph]
Bioconductor views Clustering FunctionalGenomics GeneExpression GeneRegulation GenomeAnnotation Sequencing Transcription
MaintainerR. Taylor Raborn <[email protected]>
LicenseGPL-3
Version1.1.0
URL https://github.com/brendelgroup/tsrchitect
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("Bioconductor-mirror/TSRchitect")
Bioconductor-mirror/TSRchitect documentation built on June 1, 2017, 3:20 a.m.