Files in shinyWGD

'Shiny' Application for Whole Genome Duplication Analysis

README.md R/obtain_coordinates_for_anchorpoints_ks.R R/obtain_chromosome_length.R R/clustering_synteny.R R/find_peaks_resample_95_CI.R R/from_features.R R/running_emmix.R R/runApp.R R/obtain_coordinates_for_anchorpoints.R R/SiZer.R R/obtain_coordinates_for_segments.v2.R R/ksv.R R/obtain_coordinates_for_segments.multiple_species.R R/remove_old_directories.R R/substitution_rate_correction.R R/calculateKsDistribution4wgd_multiple.v2.R R/extracting_tree_from_timetree.R R/computeAnchorPointDepth.R R/obtain_mean_ks_for_multiplicons.R R/CountOrthologs.R R/emmix.R R/utils.R inst/shinyWGD/app.R inst/shinyWGD/www/content/gallery.md inst/shinyWGD/www/content/introduction.md inst/shinyWGD/www/content/help.md inst/shinyWGD/R/obtain_coordinates_for_anchorpoints_ks.R inst/shinyWGD/R/obtain_chromosome_length.R inst/shinyWGD/R/clustering_synteny.R inst/shinyWGD/R/find_peaks_resample_95_CI.R inst/shinyWGD/R/from_features.R inst/shinyWGD/R/running_emmix.R inst/shinyWGD/R/runApp.R inst/shinyWGD/R/obtain_coordinates_for_anchorpoints.R inst/shinyWGD/R/SiZer.R inst/shinyWGD/R/obtain_coordinates_for_segments.v2.R inst/shinyWGD/R/ksv.R inst/shinyWGD/R/obtain_coordinates_for_segments.multiple_species.R inst/shinyWGD/R/remove_old_directories.R inst/shinyWGD/R/substitution_rate_correction.R inst/shinyWGD/R/calculateKsDistribution4wgd_multiple.v2.R inst/shinyWGD/R/extracting_tree_from_timetree.R inst/shinyWGD/R/computeAnchorPointDepth.R inst/shinyWGD/R/obtain_mean_ks_for_multiplicons.R inst/shinyWGD/R/CountOrthologs.R inst/shinyWGD/R/emmix.R inst/shinyWGD/R/utils.R inst/shinyWGD/tools/obtain_newick_tree_from_timetree.R inst/shinyWGD/tools/cds2aa.R inst/shinyWGD/tools/prepare_orthofinder.R inst/shinyWGD/ui/joint_tree.ui.R inst/shinyWGD/ui/gallery.ui.R inst/shinyWGD/ui/data_preparation.ui.R inst/shinyWGD/ui/extracting_tree.ui.R inst/shinyWGD/ui/whale_preparation.ui.R inst/shinyWGD/ui/introduction.ui.R inst/shinyWGD/ui/tree_reconciliation.ui.R inst/shinyWGD/ui/ks_age_distribution.ui.R inst/shinyWGD/ui/help.ui.R inst/shinyWGD/ui/synteny_analysis.ui.R inst/shinyWGD/server/gallery.server.R inst/shinyWGD/server/help.server.R inst/shinyWGD/server/tree_reconciliation.server.R inst/shinyWGD/server/data_preparation.server.R inst/shinyWGD/server/joint_tree.server.R inst/shinyWGD/server/extracting_tree.server.R inst/shinyWGD/server/introduction.server.R inst/shinyWGD/server/ks_age_distribution.server.R inst/shinyWGD/server/synteny_analysis.server.R inst/shinyWGD/server/whale_preparation.server.R tests/testthat.R tests/testthat/test-runApp.R man/modeFinder.Rd man/mix_logNormal_Ks.Rd man/symconv2D.ks.Rd man/parse_one_EMMIX.Rd man/is_fasta_cds.Rd man/SiZer.Rd man/relativeRate.Rd man/PeaksInKsDistributionValues.Rd man/check_gff_from_file.Rd man/obtain_chromosome_length_filter.Rd man/remove_old_dirs.Rd man/bootStrapPeaks.Rd man/parse_EMMIX.Rd man/downloadButton_custom.Rd man/dfltCounts.Rd man/cluster_synteny.Rd man/SignifFeatureRegion.Rd man/symconv3D.ks.Rd man/symconv4D.ks.Rd man/create_ksrates_cmd.Rd man/CalPvalue.Rd man/map_informal_name_to_latin_name.Rd man/create_ksrates_configure_file_v2.Rd man/is.ksv.Rd man/run_emmix_kmeas.Rd man/symconv.ks.Rd man/TimeTreeFecher.Rd man/calculateKsDistribution4wgd_multiple.Rd man/create_ksrates_configure_file_based_on_table.Rd man/generate_ksd.Rd man/CountOrthologs.Rd man/create_ksrates_cmd_from_table.Rd man/create_ksrates_expert_parameter_file.Rd man/generateKsDistribution.Rd man/obtain_mean_ks_for_each_multiplicon.Rd man/read.wgd_ksd.Rd man/check_gff_input.Rd man/get_segments.Rd man/obtain_coordiantes_for_segments.Rd man/read_data_file.Rd man/extractCluster.Rd man/extract_first_part.Rd man/computing_depth_paranome.Rd man/analysisEachCluster.Rd man/computing_depth.Rd man/remove_inner_stop_codon_sequence.Rd man/obtain_chromosome_length.Rd man/find_peaks.Rd man/obtain_coordiantes_for_anchorpoints_ks.Rd man/drvkde.Rd man/check_proteome_from_file.Rd man/dfltBWrange.Rd man/obtain_coordinates_for_segments_multiple.Rd man/runshinyWGD.Rd man/CalHomoConcentration.Rd man/checkFileExistence.Rd man/ks_mclust_v2.Rd man/is.not.null.Rd man/resampleKsDistribution.Rd man/obtain_coordiantes_for_anchorpoints.Rd man/replace_informal_name_to_latin_name.Rd man/check_proteome_input.Rd