Diversity Analysis for Sequence Data

Documentation for package ‘GaMaBioMD’ version 0.2.0

alignment_info	Sequence Alignment and Analysis
bubble_plot_count	Bubble Plot Count Function
bubble_plot_percentage	Bubble Plot Percentage Function
clustering_average_similarity	Perform Hierarchical Clustering for average similarity matrix
clustering_percent_similarity	Perform Hierarchical Clustering for Percent Similarity
compute_average_similarity_matrix	Compute Average Similarity Matrix
data_sampling	Samples data from each SampleID group if specified, otherwise uses the final data.
expand_accession_ranges	This function expands accession number ranges, creating a data frame with sample and accession numbers.
generate_heatmaps	Generate Heatmaps
get_sequence_information	Retrieves sequence information for a given list of accessions.
preprocess_for_alignment	Preprocesses data for sequence alignment.
SampleID_vs_NumSequences	Plots the number of sequences and the probability of sequences per SampleID.
tree_average_similarity	Generate Phylogenetic Tree and Color Palette for Average Similarity
tree_percent_similarity	Generate Phylogenetic Tree and Color Palette for Percent Similarity Matrix
write_fasta	Writes a data frame to a FASTA file.