Package: colocalized
Type: Package
Title: Clusters of Colocalized Sequences
Version: 0.2.0
Authors@R: person("Stefan", "Golas", email = "stefanmgolas@gmail.com", role = c("cre","aut"))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1.9000
Depends: R (>= 3.0.0)
Imports: foreach, doParallel, purrr, utils
NeedsCompilation: no
Packaged: 2019-10-18 00:45:17 UTC; Stefan
Author: Stefan Golas [cre, aut]
Maintainer: Stefan Golas <stefanmgolas@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-18 21:20:12 UTC
Built: R 4.4.3; ; 2025-12-08 03:45:34 UTC; windows
