CalHomoConcentration    Compute the -log10 of Poisson Distribution
CalPvalue               Compute the P-value of a Cluster using the
                        Poisson Distribution
CountOrthologs          Count Ortholog Genes in a Species
PeaksInKsDistributionValues
                        Find Peaks in the Ks Distribution
SiZer                   SiZer (Significant Zero Crossings)
SignifFeatureRegion     SignifFeatureRegion
TimeTreeFecher          Extracts a timetree from TimeTree.org based on
                        species names.
analysisEachCluster     Perform synteny analysis for identified
                        clusters
bootStrapPeaks          Bootstrap Peaks in the Ks Distribution
calculateKsDistribution4wgd_multiple
                        Calculate the Ks Distribution for Multiple
                        Speices
checkFileExistence      Check File Existence in a Data Table
check_gff_from_file     Check and Process GFF Input File from a
                        Specific Path
check_gff_input         Check and Prepare GFF/GTF Input File
check_proteome_from_file
                        Check and Process Proteome Input File From a
                        Special Path
check_proteome_input    Check and Process Proteome Input File
cluster_synteny         Cluster Synteny Data and Generate Trees
computing_depth         Compute the Depth of Anchored Points
computing_depth_paranome
                        Compute the Depth of Anchored Points in a
                        Paranome Comparison
create_ksrates_cmd      Create Ksrates Command Files from Shiny Input
create_ksrates_cmd_from_table
                        Create Ksrates Command Files from Data Table
create_ksrates_configure_file_based_on_table
                        Create Ksrates Configuration File Based on Data
                        Table
create_ksrates_configure_file_v2
                        Create Ksrates Configuration File
create_ksrates_expert_parameter_file
                        Create ksrates Expert Parameter File
dfltBWrange             dfltBWrange
dfltCounts              dfltCounts
downloadButton_custom   Creating a Custom Download Button
drvkde                  drvkde
extractCluster          Extract clusters based on specified scaffolds
extract_first_part      Extract the first part of a string by splitting
                        it at tab characters.
find_peaks              Find Peaks in a Numeric Vector
generateKsDistribution
                        Generate the Ks Distribution
generate_ksd            Generate Kernel Density Estimates (KDE) for Ks
                        Distribution
get_segments            Get Segmented Data from Anchorpoints and Ks
                        Values
is.ksv                  Check if an object is of class "ksv"
is.not.null             Check if an Object is Not NULL
is_fasta_cds            Check if a file is in FASTA format with cds
                        sequences.
ks_mclust_v2            ks_mclust_v2
map_informal_name_to_latin_name
                        Map Informal Names to Latin Names
mix_logNormal_Ks        Log-Normal mixturing analyses of a Ks
                        distributions for the whole paranome
modeFinder              modeFinder
obtain_chromosome_length
                        obtain_chromosome_length
obtain_chromosome_length_filter
                        obtain_chromosome_length_filter
obtain_coordiantes_for_anchorpoints
                        Obtain coordinates for anchorpoints from GFF
                        files
obtain_coordiantes_for_anchorpoints_ks
                        Obtain Coordinates and Ks Values for
                        Anchorpoints
obtain_coordiantes_for_segments
                        Obtain coordinates for segments in a comparison
obtain_coordinates_for_segments_multiple
                        Obtain Coordinates for Segments in Multiple
                        Synteny Blocks
obtain_mean_ks_for_each_multiplicon
                        Compute the Mean of Ks values for Each
                        Multiplicon
parse_EMMIX             Read the EMMIX output for a range of components
parse_one_EMMIX         Read the EMMIX output for a specify number of
                        components
read.wgd_ksd            Read the output file of wgd ksd
read_data_file          Read Data from Uploaded File
relativeRate            relativeRate
remove_inner_stop_codon_sequence
                        Remove Genes Contain Stop Codons within the
                        Sequence
remove_old_dirs         Remove directories older than a specified day
replace_informal_name_to_latin_name
                        Replace Informal Names with Latin Names
resampleKsDistribution
                        Resample a Ks Distribution
run_emmix_kmeas         A wrapper to run EM analysis of \(ln\) Ks
                        values with k-means
runshinyWGD             The main code to run shinyWGD
symconv.ks              symconv.ks
symconv2D.ks            symconv2D.ks
symconv3D.ks            symconv3D.ks
symconv4D.ks            symconv4D.ks
