STRAH: Short Tandem Repeats Analysis of Hotspot Zones

Searches for short tandem repeats (STR) in a specified region of any genome. This analysis can be expanded such that several regions (chromosomes) are studied. These STRs can be grouped into hotspot as well as flanking regions of user specified width. Hotspots are defined by the double strand break maps from Pratto et al. (2014) <doi:10.1126/science.1256442>. Moreover, the user can also search for a specified motif in a DNAStringSet-object, or a fasta-file, or a specified region of any genome. For an application of STR detections please see Heissl et al. (2018) <doi:10.1101/431841>.

Version: 1.0
Depends: R (≥ 2.10)
Imports: Biostrings (≥ 2.38.4), BSgenome, BSgenome.Hsapiens.UCSC.hg19, BiocManager, methods
Suggests: BSgenome.Ptroglodytes.UCSC.panTro5
Published: 2019-04-09
Author: Philipp Hermann ORCID iD [aut, cre], Monika Heinzl [aut], Angelika Heissl [ctb], Irene Tiemann-Boege ORCID iD [ctb], Andreas Futschik ORCID iD [ctb]
Maintainer: Philipp Hermann <philipp.hermann at>
License: MIT + file LICENSE
NeedsCompilation: no
CRAN checks: STRAH results


Reference manual: STRAH.pdf
Package source: STRAH_1.0.tar.gz
Windows binaries: r-devel:, r-devel-gcc8:, r-release:, r-oldrel:
OS X binaries: r-release: not available, r-oldrel: not available


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