R Packages for Biochemistry

[discoleo]

Various R packages are not included in the Task View:

• First 2 are general packages;
• Packages 3 - 7 use various statistical models to predict certain features/proteins;
• Remaining: other functions;

1. Package Peptides: https://cran.r-project.org/web/packages/Peptides/index.html
2. Package seqinr: Biological Sequences Retrieval and Analysis;
3. Package ampri: Predict antimicrobial peptides;
4. Package epitopR: Predict Peptide-MHC Binding;
5. Package CancerGram: Predict Anticancer Peptides;
6. Package signalHsmm: Predicts the presence of signal peptides in eukaryotic protein using hidden semi-Markov models;
7. Package AntAngioCOOL: Anti-Angiogenic Peptide Prediction;
8. Package LSPFP: Lysate and Secretome Peptide Feature Plotter;
9. Package helixvis: Visualize Alpha-Helical Peptide Sequences;
10. Package prozor: Minimal Protein Set Explaining Peptide Spectrum Matches;
11. Package RHybridFinder: Identification of Hybrid Peptides in Immunopeptidomic Analyses;
12. Package protag: Search Tagged Peptides & Draw Highlighted Mass Spectra;

DataBases

1. Package UniprotR: Retrieving Information of Proteins from Uniprot;

There are a few more missing. There may be some overlap with Bioconductor: it may be possible to create meaningful links to Bioconductor Task Views (and add the packges there if needed).

Algorithms

Algorithms in proteomics/genomics may also benefit from:

• see "Patricia trie" for details on the trie data structure;
  1. Package AhoCorasickTrie: Fast Searching for Multiple Keywords in Multiple Texts;
  2. Package triebeard: Radix Trees in Rcpp;

[k-m-m]

Thank you for these suggestions. In my view these peptide and protein-related packages are a better fit for the Omics task view --- https://cran.r-project.org/web/views/Omics.html -- that has a focus more on biochemistry.