Host-Pathogen Interaction Prediction

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Documentation for package ‘HPiP’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calculateAAC	Calculate Amino Acid Composition (AAC) Descriptor
calculateAutocor	Calculate Autocorrelation Descriptors
calculateBE	Tranform a Seqeuence into Binary Encoding (BE)
calculateCTDC	Calculate CTD Descriptors - Composition (C)
calculateCTDD	Calculate CTD Descriptors - Distribution (D)
calculateCTDT	Calculate CTD Descriptors - Transition (T)
calculateCTriad	Calculate Conjoint Triad Descriptor
calculateDC	Calculate Dipeptide Composition (DC) Descriptor
calculateF	Calculate F1 or F2 Descriptors
calculateKSAAP	Calculate k-spaced Amino Acid Pairs (KSAAP) Descriptor
calculateQD_Sm	Calculate Quadruples Composition (QC) Descriptor from Biochemical Similarity Classes
calculateTC	Calculate Tripeptide Composition (TC) Descriptor
calculateTC_Sm	Calculate Tripeptide Composition (TC) Descriptor from Biochemical Similarity Classes
corr_plot	Plot Correlation Matrix between Input Features
enrich.df	Enrichment Result
enrichfindP	Functional Enrichment Analysis for Pathogen Interactors in the High-Confidence Network.
enrichfind_cpx	Functional Enrichment Analysis for Predicted Modules
enrichfind_hp	Functional Enrichment Analysis of all Host Proteins
enrichplot	Plot the Enrichment Reuslt
example_data	Input Data for Prediction Algorithm
filter_missing_values	Drop the Missing Values Above a Certain Threshold
FreqInteractors	Plot the Pathogen Proteins' frequency of Interactions with Host Proteins
FSmethod	Feature Selection via Matrix Correlation and Recursive Feature Elimination (RFE)
getFASTA	Fetch FASTA Sequence from the UniProt Database
getHPI	Generating Host-Pathogen Protein-Protein Interaction (HP-PPI) Descriptors
get_negativePPI	Construct Negative Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs)
get_positivePPI	Fetch Positive Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs) from the BioGRID Database
Gold_ReferenceSet	Gold-standard Reference Set of Inter-Species PPIs
host_se	Host SummarizedExperiment object
impute_missing_data	Impute missing Values per Features (i.e., Columns)
plotPPI	Plot the Predicted PPI
predicted_PPIs	Predicted HP-PPIs
pred_ensembel	Predict Interactions via Ensemble Learning Method
run_clustering	Module Detection
unlabel_data	HP-PPIs with Unknown Class Labels
UP000464024_df	Data.frame Containing SARS-CoV-2 FASTA Sequences
var_imp	Variable Importance Plot
viral_se	Viral SummarizedExperiment object