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 |
| Author: |
Stefan Golas [cre, aut] |
| Maintainer: |
Stefan Golas <stefanmgolas at gmail.com> |
| License: |
MIT + file LICENSE |
| NeedsCompilation: |
no |
| CRAN checks: |
colocalized results |
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=colocalized
to link to this page.