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 <>. 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.

Getting started

Package details

AuthorStefan Golas [cre, aut]
MaintainerStefan Golas <>
LicenseMIT + file LICENSE
Package repositoryView on CRAN
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colocalized documentation built on Oct. 30, 2019, 10:49 a.m.