pqsfinder: Identification of potential quadruplex forming sequences

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The main functionality of the this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, this package is able to detect sequences responsible for G4s folded from imperfect G-runs containing bulges or mismatches and as such is more sensitive than competing algorithms.

Author
Jiri Hon, Matej Lexa and Tomas Martinek
Date of publication
None
Maintainer
Jiri Hon <jiri.hon@gmail.com>
License
BSD_2_clause + file LICENSE
Version
1.2.3

View on Bioconductor

Man pages

as.character-PQSViews-method
Coerce to character vector
density-PQSViews-method
Get density vector
pqsfinder
Identificate potential quadruplex forming sequences.
PQSViews
PQSViews class constructor.
PQSViews-class
An S4 class to represent potential quadruplex forming...
score-PQSViews-method
Get PQS score vector
show-PQSViews-method
Show method
strand-PQSViews-method
Get PQS strand vector

Files in this package

pqsfinder/DESCRIPTION
pqsfinder/LICENSE
pqsfinder/NAMESPACE
pqsfinder/NEWS
pqsfinder/R
pqsfinder/R/PQSViews-class.R
pqsfinder/R/RcppExports.R
pqsfinder/build
pqsfinder/build/vignette.rds
pqsfinder/inst
pqsfinder/inst/doc
pqsfinder/inst/doc/pqsfinder.R
pqsfinder/inst/doc/pqsfinder.Rmd
pqsfinder/inst/doc/pqsfinder.html
pqsfinder/man
pqsfinder/man/PQSViews-class.Rd
pqsfinder/man/PQSViews.Rd
pqsfinder/man/as.character-PQSViews-method.Rd
pqsfinder/man/density-PQSViews-method.Rd
pqsfinder/man/pqsfinder.Rd
pqsfinder/man/score-PQSViews-method.Rd
pqsfinder/man/show-PQSViews-method.Rd
pqsfinder/man/strand-PQSViews-method.Rd
pqsfinder/src
pqsfinder/src/Makevars
pqsfinder/src/RcppExports.cpp
pqsfinder/src/boost_regex
pqsfinder/src/boost_regex/c_regex_traits.cpp
pqsfinder/src/boost_regex/c_regex_traits.o
pqsfinder/src/boost_regex/cpp_regex_traits.cpp
pqsfinder/src/boost_regex/cpp_regex_traits.o
pqsfinder/src/boost_regex/cregex.cpp
pqsfinder/src/boost_regex/cregex.o
pqsfinder/src/boost_regex/fileiter.cpp
pqsfinder/src/boost_regex/fileiter.o
pqsfinder/src/boost_regex/icu.cpp
pqsfinder/src/boost_regex/icu.o
pqsfinder/src/boost_regex/instances.cpp
pqsfinder/src/boost_regex/instances.o
pqsfinder/src/boost_regex/internals.hpp
pqsfinder/src/boost_regex/posix_api.cpp
pqsfinder/src/boost_regex/posix_api.o
pqsfinder/src/boost_regex/regex.cpp
pqsfinder/src/boost_regex/regex.o
pqsfinder/src/boost_regex/regex_debug.cpp
pqsfinder/src/boost_regex/regex_debug.o
pqsfinder/src/boost_regex/regex_raw_buffer.cpp
pqsfinder/src/boost_regex/regex_raw_buffer.o
pqsfinder/src/boost_regex/regex_traits_defaults.cpp
pqsfinder/src/boost_regex/regex_traits_defaults.o
pqsfinder/src/boost_regex/static_mutex.cpp
pqsfinder/src/boost_regex/static_mutex.o
pqsfinder/src/boost_regex/usinstances.cpp
pqsfinder/src/boost_regex/usinstances.o
pqsfinder/src/boost_regex/w32_regex_traits.cpp
pqsfinder/src/boost_regex/w32_regex_traits.o
pqsfinder/src/boost_regex/wc_regex_traits.cpp
pqsfinder/src/boost_regex/wc_regex_traits.o
pqsfinder/src/boost_regex/wide_posix_api.cpp
pqsfinder/src/boost_regex/wide_posix_api.o
pqsfinder/src/boost_regex/winstances.cpp
pqsfinder/src/boost_regex/winstances.o
pqsfinder/src/pqs_cache.h
pqsfinder/src/pqs_storage.h
pqsfinder/src/pqsfinder.cpp
pqsfinder/src/results.h
pqsfinder/vignettes
pqsfinder/vignettes/pqsfinder.Rmd
pqsfinder/vignettes/pqsfinder.bib