To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TSRchitect")

In most cases, you don't need to download the package archive at all.

TSRchitect

DOI: 10.18129/B9.bioc.TSRchitect    

This is the development version of TSRchitect; for the stable release version, see TSRchitect.

Promoter identification from large-scale TSS profiling data

Bioconductor version: Development (3.7)

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). In addition, (new with version 1.2.0) TSRchitect provides the ability to import aligned EST and cDNA data. 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.

Author: R. Taylor Raborn [aut, cre, cph] Volker P. Brendel [aut, cph] Krishnakumar Sridharan [ctb]

Maintainer: R. Taylor Raborn <rtraborn at indiana.edu>

Citation (from within R, enter citation("TSRchitect")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TSRchitect")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TSRchitect")

 

PDF TSRchitect User's Guide
HTML TSRchitect User's Guide
HTML R Script TSRchitect vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, FunctionalGenomics, GeneExpression, GeneRegulation, GenomeAnnotation, Sequencing, Software, Transcription
Version 1.5.0
In Bioconductor since BioC 3.5 (R-3.4) (0.5 years)
License GPL-3
Depends R (>= 3.4)
Imports AnnotationHub, BiocGenerics, BiocParallel, GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools, IRanges, methods, Rsamtools(>= 1.14.3), rtracklayer, S4Vectors, SummarizedExperiment, utils
LinkingTo
Suggests ENCODExplorer, ggplot2, knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/brendelgroup/tsrchitect
BugReports https://github.com/brendelgroup/tsrchitect/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TSRchitect_1.5.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) TSRchitect_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TSRchitect
Package Short Url http://bioconductor.org/packages/TSRchitect/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: