DOI: 10.18129/B9.bioc.TSRchitect    

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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: 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>

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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
Suggests ENCODExplorer, ggplot2, knitr, rmarkdown
URL https://github.com/brendelgroup/tsrchitect
BugReports https://github.com/brendelgroup/tsrchitect/issues
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