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Contains utilities for the analysis of post-translational modifications (PTMs) in proteins, with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download, filter and analyze data from the sulfoxidation database 'MetOSite'. Utilities to search and characterize S-aromatic motifs in proteins are also provided. In addition, functions to analyze sequence environments around modifiable residues in proteins can be found. For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable residues from the proteins of interest. Functions tailored to test statistical hypothesis related to these differential sequence environments are also implemented. Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).
| Version: | 1.0.1 |
| Depends: | R (≥ 4.0.0) |
| Imports: | bio3d (≥ 2.3-4), curl, graphics, httr, jsonlite, stats |
| Suggests: | knitr, markdown, testthat |
| Published: | 2024-05-21 |
| DOI: | 10.32614/CRAN.package.ptm |
| Author: | Juan Carlos Aledo [aut, cre] |
| Maintainer: | Juan Carlos Aledo <caledo at uma.es> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://bitbucket.org/jcaledo/ptm, https://github.com/jcaledo/Rptm, https://metositeptm.com |
| NeedsCompilation: | no |
| Citation: | ptm citation info |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | ptm results |
| Reference manual: | ptm.pdf |
| Package source: | ptm_1.0.1.tar.gz |
| Windows binaries: | r-devel: ptm_1.0.1.zip, r-release: ptm_1.0.1.zip, r-oldrel: ptm_1.0.1.zip |
| macOS binaries: | r-release (arm64): ptm_1.0.1.tgz, r-oldrel (arm64): ptm_1.0.1.tgz, r-release (x86_64): ptm_1.0.1.tgz, r-oldrel (x86_64): ptm_1.0.1.tgz |
| Old sources: | ptm archive |
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