Description
A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
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CRAN Check Status
14
NOTE
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | NOTE |
| r-release-macos-x86_64 | NOTE |
| r-release-windows-x86_64 | NOTE |
Check details (14 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
Check History
NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc},
| ^