Man pages for shinyWGD
'Shiny' Application for Whole Genome Duplication Analysis
| 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... |
| 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... |
| find_peaks | Find Peaks in a Numeric Vector |
| generate_ksd | Generate Kernel Density Estimates (KDE) for Ks Distribution |
| generateKsDistribution | Generate the Ks Distribution |
| get_segments | Get Segmented Data from Anchorpoints and Ks Values |
| is_fasta_cds | Check if a file is in FASTA format with cds sequences. |
| is.ksv | Check if an object is of class "ksv" |
| is.not.null | Check if an Object is Not NULL |
| 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... |
| 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_data_file | Read Data from Uploaded File |
| read.wgd_ksd | Read the output file of wgd ksd |
| 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 |
| SignifFeatureRegion | SignifFeatureRegion |
| SiZer | SiZer (Significant Zero Crossings) |
| symconv2D.ks | symconv2D.ks |
| symconv3D.ks | symconv3D.ks |
| symconv4D.ks | symconv4D.ks |
| symconv.ks | symconv.ks |
| TimeTreeFecher | Extracts a timetree from TimeTree.org based on species names. |
