Package: colocalized 0.2.0
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.
Authors:
colocalized_0.2.0.tar.gz
colocalized_0.2.0.zip(r-4.5)colocalized_0.2.0.zip(r-4.4)colocalized_0.2.0.zip(r-4.3)
colocalized_0.2.0.tgz(r-4.5-any)colocalized_0.2.0.tgz(r-4.4-any)colocalized_0.2.0.tgz(r-4.3-any)
colocalized_0.2.0.tar.gz(r-4.5-noble)colocalized_0.2.0.tar.gz(r-4.4-noble)
colocalized_0.2.0.tgz(r-4.4-emscripten)colocalized_0.2.0.tgz(r-4.3-emscripten)
colocalized.pdf |colocalized.html✨
colocalized/json (API)
| # Install 'colocalized' in R: |
| install.packages('colocalized', repos = c('https://stefangolas.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:496527ec2f. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-win | OK | Feb 28 2025 |
| R-4.5-mac | OK | Feb 28 2025 |
| R-4.5-linux | OK | Feb 28 2025 |
| R-4.4-win | OK | Feb 28 2025 |
| R-4.4-mac | OK | Feb 28 2025 |
| R-4.3-win | OK | Feb 28 2025 |
| R-4.3-mac | OK | Feb 28 2025 |
Exports:chromsearchcolocalizedcolocalized_sequentialColocalizedFullSearchgensearchonedim_dist
Dependencies:clicodetoolsdoParallelforeachglueiteratorslifecyclemagrittrpurrrrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Search one chromsome | chromsearch |
| Colocalized cluster search. | colocalized |
| Sequential cluster search | colocalized_sequential |
| Colocalized full search. | ColocalizedFullSearch |
| Whole genome search. | gensearch |
| NFKB1 bed file | nfkb1 |
| NFKB2 bed file | nfkb2 |
| Create a colocalization matrix | onedim_dist |
| RELB bed file | relb |
