TSRchitect

DOI: 10.18129/B9.bioc.TSRchitect    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TSRchitect.

Promoter identification from large-scale TSS profiling data

Bioconductor version: Release (3.15)

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, STRIPE-seq). In addition, (new with version 1.3.0) 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 two forms of the 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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TSRchitect")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Clustering, FunctionalGenomics, GeneExpression, GeneRegulation, GenomeAnnotation, Sequencing, Software, Transcription
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
License	GPL-3
Depends	R (>= 3.5)
Imports	AnnotationHub, BiocGenerics, BiocParallel, dplyr, GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools, IRanges, methods, readxl, Rsamtools(>= 1.14.3), rtracklayer, S4Vectors, SummarizedExperiment, tools, utils
LinkingTo
Suggests	ENCODExplorer, ggplot2, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/brendelgroup/tsrchitect
BugReports	https://github.com/brendelgroup/tsrchitect/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/TSRchitect
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TSRchitect
Package Short Url	https://bioconductor.org/packages/TSRchitect/
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