'Shiny' Application for Whole Genome Duplication Analysis


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Documentation for package ‘shinyWGD’ version 1.0.0

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analysisEachCluster Perform synteny analysis for identified clusters
bootStrapPeaks Bootstrap Peaks in the Ks Distribution
calculateKsDistribution4wgd_multiple Calculate the Ks Distribution for Multiple Speices
CalHomoConcentration Compute the -log10 of Poisson Distribution
CalPvalue Compute the P-value of a Cluster using the Poisson Distribution
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
CountOrthologs Count Ortholog Genes in a Species
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
PeaksInKsDistributionValues Find Peaks in the Ks Distribution
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
runshinyWGD The main code to run shinyWGD
run_emmix_kmeas A wrapper to run EM analysis of \(ln\) Ks values with k-means
SignifFeatureRegion SignifFeatureRegion
SiZer SiZer (Significant Zero Crossings)
symconv.ks symconv.ks
symconv2D.ks symconv2D.ks
symconv3D.ks symconv3D.ks
symconv4D.ks symconv4D.ks
TimeTreeFecher Extracts a timetree from TimeTree.org based on species names.