colocalized: Clusters of Colocalized Sequences

Also abbreviates to "CCSeq". Finds clusters of colocalized sequences in .bed annotation files up to a specified cut-off distance. Two sequences are colocalized if they are within the cut-off distance of each other, and clusters are sets of sequences where each sequence is colocalized to at least one other sequence in the cluster. For a set of .bed annotation tables provided in a list along with a cut-off distance, the program will output a file containing the locations of each cluster. Annotated .bed files are from the 'pwmscan' application at <https://ccg.epfl.ch/pwmtools/pwmscan.php>. Personal machines might crash or take excessively long depending on the number of annotated sequences in each file and whether chromsearch() or gensearch() is used.

Version:	0.2.0
Depends:	R (≥ 3.0.0)
Imports:	foreach, doParallel, purrr, utils
Published:	2019-10-18
DOI:	10.32614/CRAN.package.colocalized
Author:	Stefan Golas [cre, aut]
Maintainer:	Stefan Golas <stefanmgolas at gmail.com>
License:	MIT + file LICENSE
NeedsCompilation:	no
CRAN checks:	colocalized results

Documentation:

Reference manual:

colocalized.html , colocalized.pdf

Downloads:

Package source:	colocalized_0.2.0.tar.gz
Windows binaries:	r-devel: colocalized_0.2.0.zip, r-release: colocalized_0.2.0.zip, r-oldrel: colocalized_0.2.0.zip
macOS binaries:	r-release (arm64): colocalized_0.2.0.tgz, r-oldrel (arm64): colocalized_0.2.0.tgz, r-release (x86_64): colocalized_0.2.0.tgz, r-oldrel (x86_64): colocalized_0.2.0.tgz
Old sources:	colocalized archive

Linking:

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