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Table 1 Description of PDAUG tools. PDAUG toolset comprises 24 different tools across 9 functional categories

From: PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

Functionality Tool name Major libraries used
Data visualization and plotting PDAUG basic plots matplotlib*, pandas*, seaborn*, quantiprot
PDAUG fishers plot
PDAUG peptide data plotting
PDAUG peptide Ngrams
PDAUG sequence network
PDAUG peptide length distribution
PDAUG uversky plot
Descriptor calculation PDAUG AA property based peptide descriptor modlAMP, pandas, pydpi
PDAUG peptide core descriptors
PDAUG peptide global descriptors
PDAUG sequence property based descriptors
PDAUG word vector descriptor
Peptide library generation PDAUG AA property based peptide generation modlAMP, pandas
PDAUG sequence based peptide generation
ML PDAUG ML models sklearn*, matplotlib, seaborn, pandas, gensim, nltk
PDAUG word vector model
Circular dichroism (CD) data analysis PDAUG peptide CD spectral analysis modlAMP, pandas
Peptide 3D structure PDAUG peptide structure builder fragbuilder, pandas
Core functionality PDAUG peptide sequence analysis modlAMP, pandas
PDAUG peptide core functions
Peptide data access PDAUG peptide data access modlAMP, biopython, pandas
Data handling and IO PDAUG TSVtoFASTA pandas
PDAUG merge dataframes
PDAUG AddClassLabel
  1. Libraries utilized for functionally important tasks are listed for each tool
  2. *Python libraries used in data science