Predict Antimicrobial Peptides

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Documentation for package ‘ampir’ version 1.0.0

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aaseq_is_valid Check protein sequences for non-standard amino acids
calculate_features Calculate a set of numerical features from protein sequences
calc_amphiphilicity Calculate amphiphilicity (or hydrophobic moment)
calc_hydrophobicity Calculate the hydrophobicity
calc_mw Calculate the molecular weight
calc_net_charge Calculate the net charge
calc_pI Calculate the isoelectric point (pI)
calc_pseudo_comp Calculate the pseudo amino acid composition
chunk_rows Determine row breakpoints for dividing a dataset into chunks for parallel processing
df_to_faa Save a dataframe in FASTA format
predict_amps Predict the antimicrobial peptide probability of a protein
read_faa Read FASTA amino acids file into a dataframe
remove_nonstandard_aa Remove non standard amino acids from protein sequences