Man pages for mrbakhsh/HPiP
Host-Pathogen Interaction Prediction
| 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... |
| calculateTC | Calculate Tripeptide Composition (TC) Descriptor |
| calculateTC_Sm | Calculate Tripeptide Composition (TC) Descriptor from... |
| corr_plot | Plot Correlation Matrix between Input Features |
| enrich.df | Enrichment Result |
| enrichfind_cpx | Functional Enrichment Analysis for Predicted Modules |
| enrichfind_hp | Functional Enrichment Analysis of all Host Proteins |
| enrichfindP | Functional Enrichment Analysis for Pathogen Interactors in... |
| 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... |
| FSmethod | Feature Selection via Matrix Correlation and Recursive... |
| getFASTA | Fetch FASTA Sequence from the UniProt Database |
| getHPI | Generating Host-Pathogen Protein-Protein Interaction (HP-PPI)... |
| get_negativePPI | Construct Negative Reference Host-Pathogen Protein-Protein... |
| get_positivePPI | Fetch Positive Reference Host-Pathogen Protein-Protein... |
| 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 |
| pred_ensembel | Predict Interactions via Ensemble Learning Method |
| predicted_PPIs | Predicted HP-PPIs |
| 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 |
