Man pages for shinyWGD
'Shiny' Application for Whole Genome Duplication Analysis

analysisEachClusterPerform synteny analysis for identified clusters
bootStrapPeaksBootstrap Peaks in the Ks Distribution
calculateKsDistribution4wgd_multipleCalculate the Ks Distribution for Multiple Speices
CalHomoConcentrationCompute the -log10 of Poisson Distribution
CalPvalueCompute the P-value of a Cluster using the Poisson...
checkFileExistenceCheck File Existence in a Data Table
check_gff_from_fileCheck and Process GFF Input File from a Specific Path
check_gff_inputCheck and Prepare GFF/GTF Input File
check_proteome_from_fileCheck and Process Proteome Input File From a Special Path
check_proteome_inputCheck and Process Proteome Input File
cluster_syntenyCluster Synteny Data and Generate Trees
computing_depthCompute the Depth of Anchored Points
computing_depth_paranomeCompute the Depth of Anchored Points in a Paranome Comparison
CountOrthologsCount Ortholog Genes in a Species
create_ksrates_cmdCreate Ksrates Command Files from Shiny Input
create_ksrates_cmd_from_tableCreate Ksrates Command Files from Data Table
create_ksrates_configure_file_based_on_tableCreate Ksrates Configuration File Based on Data Table
create_ksrates_configure_file_v2Create Ksrates Configuration File
create_ksrates_expert_parameter_fileCreate ksrates Expert Parameter File
dfltBWrangedfltBWrange
dfltCountsdfltCounts
downloadButton_customCreating a Custom Download Button
drvkdedrvkde
extractClusterExtract clusters based on specified scaffolds
extract_first_partExtract the first part of a string by splitting it at tab...
find_peaksFind Peaks in a Numeric Vector
generate_ksdGenerate Kernel Density Estimates (KDE) for Ks Distribution
generateKsDistributionGenerate the Ks Distribution
get_segmentsGet Segmented Data from Anchorpoints and Ks Values
is_fasta_cdsCheck if a file is in FASTA format with cds sequences.
is.ksvCheck if an object is of class "ksv"
is.not.nullCheck if an Object is Not NULL
ks_mclust_v2ks_mclust_v2
map_informal_name_to_latin_nameMap Informal Names to Latin Names
mix_logNormal_KsLog-Normal mixturing analyses of a Ks distributions for the...
modeFindermodeFinder
obtain_chromosome_lengthobtain_chromosome_length
obtain_chromosome_length_filterobtain_chromosome_length_filter
obtain_coordiantes_for_anchorpointsObtain coordinates for anchorpoints from GFF files
obtain_coordiantes_for_anchorpoints_ksObtain Coordinates and Ks Values for Anchorpoints
obtain_coordiantes_for_segmentsObtain coordinates for segments in a comparison
obtain_coordinates_for_segments_multipleObtain Coordinates for Segments in Multiple Synteny Blocks
obtain_mean_ks_for_each_multipliconCompute the Mean of Ks values for Each Multiplicon
parse_EMMIXRead the EMMIX output for a range of components
parse_one_EMMIXRead the EMMIX output for a specify number of components
PeaksInKsDistributionValuesFind Peaks in the Ks Distribution
read_data_fileRead Data from Uploaded File
read.wgd_ksdRead the output file of wgd ksd
relativeRaterelativeRate
remove_inner_stop_codon_sequenceRemove Genes Contain Stop Codons within the Sequence
remove_old_dirsRemove directories older than a specified day
replace_informal_name_to_latin_nameReplace Informal Names with Latin Names
resampleKsDistributionResample a Ks Distribution
run_emmix_kmeasA wrapper to run EM analysis of \(ln\) Ks values with k-means
runshinyWGDThe main code to run shinyWGD
SignifFeatureRegionSignifFeatureRegion
SiZerSiZer (Significant Zero Crossings)
symconv2D.kssymconv2D.ks
symconv3D.kssymconv3D.ks
symconv4D.kssymconv4D.ks
symconv.kssymconv.ks
TimeTreeFecherExtracts a timetree from TimeTree.org based on species names.
shinyWGD documentation built on April 4, 2025, 2:28 a.m.