R: 'Shiny' Application for Whole Genome Duplication Analysis

# 'Shiny' Application for Whole Genome Duplication Analysis

## Documentation for package ‘shinyWGD’ version 1.0.0

- DESCRIPTION file
- Package README

## Help Pages

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.