The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
A multi-purpose and flexible k-meric enrichment analysis software. 'kmeRtone' measures the enrichment of k-mers by comparing the population of k-mers in the case loci with a carefully devised internal negative control group, consisting of k-mers from regions close to, yet sufficiently distant from, the case loci to mitigate any potential sequencing bias. This method effectively captures both the local sequencing variations and broader sequence influences, while also correcting for potential biases, thereby ensuring more accurate analysis. The core functionality of 'kmeRtone' is the SCORE() function, which calculates the susceptibility scores for k-mers in case and control regions. Case regions are defined by the genomic coordinates provided in a file by the user and the control regions can be constructed relative to the case regions or provided directly. The k-meric susceptibility scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is highly flexible by allowing users to also specify their target k-mer patterns and quantify the corresponding k-mer enrichment scores in the context of these patterns, allowing for a more comprehensive approach to understanding the functional implications of specific DNA sequences on a genomic scale (e.g., CT motifs upon UV radiation damage). Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).
| Version: | 1.0 |
| Depends: | R (≥ 4.2) |
| Imports: | data.table (≥ 1.15.0), R6 (≥ 2.5.1), Rcpp (≥ 1.0.12), R.utils (≥ 2.12.3), openxlsx (≥ 4.2.5.2), png (≥ 0.1-8), RcppSimdJson (≥ 0.1.11), venneuler (≥ 1.1-4), stringi, curl, future, future.apply, jsonlite, progressr, Biostrings, seqLogo |
| LinkingTo: | Rcpp, stringi |
| Suggests: | rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2024-08-30 |
| DOI: | 10.32614/CRAN.package.kmeRtone |
| Author: | Adib Abdullah [aut], Patrick Pflughaupt [aut], Aleksandr Sahakyan [aut, cre] |
| Maintainer: | Aleksandr Sahakyan <sahakyanlab at cantab.net> |
| BugReports: | https://github.com/SahakyanLab/kmeRtone/issues |
| License: | GPL-3 |
| URL: | https://github.com/SahakyanLab/kmeRtone |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Materials: | README |
| CRAN checks: | kmeRtone results |
| Reference manual: | kmeRtone.pdf |
| Package source: | kmeRtone_1.0.tar.gz |
| Windows binaries: | r-devel: kmeRtone_1.0.zip, r-release: kmeRtone_1.0.zip, r-oldrel: kmeRtone_1.0.zip |
| macOS binaries: | r-release (arm64): kmeRtone_1.0.tgz, r-oldrel (arm64): not available, r-release (x86_64): kmeRtone_1.0.tgz, r-oldrel (x86_64): not available |
Please use the canonical form https://CRAN.R-project.org/package=kmeRtone to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.