colocalized: Clusters of Colocalized Sequences

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: 0.1.0
Depends: R (≥ 3.0.0)
Imports: foreach, doParallel, purrr, utils
Published: 2019-09-19
Author: Stefan Golas [cre, aut]
Maintainer: Stefan Golas <stefanmgolas at gmail.com>
License: MIT + file LICENSE
NeedsCompilation: no
CRAN checks: colocalized results

Downloads:

Reference manual: colocalized.pdf
Package source: colocalized_0.1.0.tar.gz
Windows binaries: r-devel: colocalized_0.1.0.zip, r-release: colocalized_0.1.0.zip, r-oldrel: colocalized_0.1.0.zip
OS X binaries: r-release: colocalized_0.1.0.tgz, r-oldrel: colocalized_0.1.0.tgz

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