A Computational Pipeline for Entropy-Informed Detection of
Emerging Viral Variants
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Documentation for package ‘ViralEntropR’ version 0.6.2
Help Pages
| calculate_entropy | Calculate Shannon Entropy |
| calculate_hellinger_matrix | Calculate Hellinger Distance Matrix |
| cluster_sites_by_entropy | Cluster a Univariate Numeric Vector by Gaussian Mixture Model |
| decode_aa_sequence | Decode Amino Acid Sequences |
| detect_changepoints_ecp | Detect Temporal Change Points (ECP) |
| detect_changepoints_hdcp | Detect Temporal Change Points (HDcpDetect) |
| encode_aa_sequence | Encode Amino Acid Sequences |
| extract_fasta_countries | Extract Countries from FASTA Sequence Names |
| extract_fasta_dates | Extract Dates from FASTA Sequence Names |
| fasta_to_char_matrix | Convert FASTA Object to Character Matrix |
| filter_ambiguous_sequences | Remove Sequences Containing Ambiguous Residues |
| partition_time_windows | Partition Data into Time Windows |
| plot_entropy_trajectories | Plot Shannon Entropy Trajectories |
| plot_site_class_trajectory | Plot GMM Entropy Class Trajectory for a Single Site |
| relabel_entropy_classes | Relabel Entropy Classes |
| sarscov2_sample | SARS-CoV-2 Surface Glycoprotein Sequences - NCBI Demo Sample |
| sarscov2_variants | SARS-CoV-2 VOC/VOI Curated Variant Metadata |
| simulate_variant_evolution | Simulate Viral Variant Evolution |
| tabulate_site_evolution | Tabulate Site Frequency Evolution |