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ptm
View on CRAN: Click
here
Download and install ptm package within the R console
Install from CRAN:
install.packages("ptm")
Install from Github:
library("remotes")
install_github("cran/ptm")
Install by package version:
library("remotes")
install_version("ptm", "1.0.1")
Attach the package and use:
library("ptm")
Maintained by
Juan Carlos Aledo
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-12-16
Latest Update: 2022-08-07
Description:
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', and integrate data from other main PTMs
(other databases). 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. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) ).
How to cite:
Juan Carlos Aledo (2020). ptm: Analyses of Protein Post-Translational Modifications. R package version 1.0.1, https://cran.r-project.org/web/packages/ptm. Accessed 06 Nov. 2024.
Previous versions and publish date:
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Other R packages that ptm depends,
imports, suggests or enhances
Complete documentation for ptm
Functions, R codes and Examples using
the ptm R package
Some associated functions: aa.at . aa.comp . abundance . ac.scan . acc.dssp . atom.dpx . bg.go . ddG.profile . ddG.ptm . dis.scan . dot-get.exepath . dot-get.url . dpx . env.Ztest . env.extract . env.matrices . env.plot . find.aaindex . foldx.assembly . foldx.mut . foldx.stab . get.area . get.go . get.seq . gl.scan . gracefully_fail . hdfisher.go . hmeto . id.features . id.mapping . imutant . is.at . kegg.uniprot . me.scan . meto.list . meto.scan . meto.search . mkdssp . msa . net.go . ni.scan . p.scan . pairwise.dist . parse.dssp . pdb.chain . pdb.quaternary . pdb.select . pdb.seq . pdb.uniprot . pdb2uniprot . prot2codon . ptm.plot . ptm.scan . reg.scan . renum.meto . renum . renum.pdb . res.dpx . saro.dist . saro.geometry . saro.motif . search.go . sni.scan . species.kegg . species.mapping . stru.part . su.scan . term.go . ub.scan . uniprot.kegg . uniprot.pdb . uniprot2pdb . xprod .
Some associated R codes: Non-Exportable-Functions.R . aa.R . abundance.R . accdpx.R . ddG.R . distances.R . environment.R . evolutionary.R . getseq.R . go.R . gracefully.R . hmeto.R . metosite.R . ptmScan.R . ptmplot.R . saromatic.R . Full ptm package functions and examples
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