DESCRIPTION

Package: TSRchitect
Version: 1.17.3
Date: 2021-02-12
Title: Promoter identification from large-scale TSS profiling data
Description: 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.
Authors@R: c(person("R. Taylor","Raborn",email="rtraborn@indiana.edu",role=c("aut","cre","cph")),
             person("Volker","Brendel",email="vbrendel@indiana.edu",role=c("aut","cph")),
	     person("Krishnakumar","Sridharan",email="krishnakumar28@gmail.com",role="ctb"))
Author: R. Taylor Raborn [aut, cre, cph]
    Volker P. Brendel [aut, cph]
    Krishnakumar Sridharan [ctb]
Maintainer: R. Taylor Raborn <rtraborn@indiana.edu>
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
License: GPL-3
URL: https://github.com/brendelgroup/tsrchitect
BugReports: https://github.com/brendelgroup/tsrchitect/issues
Suggests:
    ENCODExplorer,
    ggplot2,
    knitr,
    rmarkdown
biocViews: Clustering, FunctionalGenomics, GeneExpression,
    GeneRegulation, GenomeAnnotation, Sequencing, Transcription
VignetteBuilder: knitr
RoxygenNote: 7.0.2
NeedsCompilation: no