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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 |
| Reference manual: | colocalized.pdf |
| 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 |
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