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colocalized  

Clusters of Colocalized Sequences
View on CRAN: Click here


Download and install colocalized package within the R console
Install from CRAN:
install.packages("colocalized")

Install from Github:
library("remotes")
install_github("cran/colocalized")

Install by package version:
library("remotes")
install_version("colocalized", "0.2.0")



Attach the package and use:
library("colocalized")
Maintained by
Stefan Golas
[Scholar Profile | Author Map]
First Published: 2019-09-19
Latest Update: 2019-10-18
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 . 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.
How to cite:
Stefan Golas (2019). colocalized: Clusters of Colocalized Sequences. R package version 0.2.0, https://cran.r-project.org/web/packages/colocalized. Accessed 30 Apr. 2025.
Previous versions and publish date:
0.1.0 (2019-09-19 11:00)
Other packages that cited colocalized R package
View colocalized citation profile
Other R packages that colocalized depends, imports, suggests or enhances
Complete documentation for colocalized
Functions, R codes and Examples using the colocalized R package
Some associated functions: ColocalizedFullSearch . chromsearch . colocalized . colocalized_sequential . gensearch . nfkb1 . nfkb2 . onedim_dist . relb . 
Some associated R codes: chromsearch.R . colocalized.R . gensearch.R . nfkb1.R . nfkb2.R . onedim_dist.R . relb.R .  Full colocalized package functions and examples
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