Files in shinyWGD
'Shiny' Application for Whole Genome Duplication Analysis

MD5
README.md
NAMESPACE
DESCRIPTION
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/myStyle.css
inst/shinyWGD/www/sand_clock_loader.css
inst/shinyWGD/www/custom.css
inst/shinyWGD/www/sand_clock_loader.html
inst/shinyWGD/www/content/scientific_names.xls
inst/shinyWGD/www/content/wgd_time_table_example.xls
inst/shinyWGD/www/content/gallery.md
inst/shinyWGD/www/content/validated_WGD_dates.info.xls
inst/shinyWGD/www/content/4sp_data_file_example.xls
inst/shinyWGD/www/content/species_name_example.xls
inst/shinyWGD/www/content/41_plant_genomes_wgd_info.xls
inst/shinyWGD/www/content/ks_peaks_example.xls
inst/shinyWGD/www/content/introduction.md inst/shinyWGD/www/content/help.md
inst/shinyWGD/www/js/iadhore.synteny.js
inst/shinyWGD/www/js/findOutgroup.js
inst/shinyWGD/www/js/webpack.conf.js
inst/shinyWGD/www/js/d3.min.js
inst/shinyWGD/www/js/popper.v2.11.5.min.js
inst/shinyWGD/www/js/figtree.js
inst/shinyWGD/www/js/clustering.js
inst/shinyWGD/www/js/tippy-bundle.umd.v6.3.7.min.js
inst/shinyWGD/www/js/Ksdistribution.js
inst/shinyWGD/www/js/progress_bar.js
inst/shinyWGD/www/images/Whale_output.jpg
inst/shinyWGD/www/images/question-solid.svg
inst/shinyWGD/www/images/logo_lab.svg
inst/shinyWGD/www/images/sticker_server.png
inst/shinyWGD/www/images/microscope-solid.svg
inst/shinyWGD/www/images/house-solid.svg
inst/shinyWGD/www/images/ksTreeIcon.svg
inst/shinyWGD/www/images/ksTree.Plot.svg
inst/shinyWGD/www/images/terminal-solid.svg
inst/shinyWGD/www/images/speciesTree.updated.whale.svg
inst/shinyWGD/www/images/sticker_github.png
inst/shinyWGD/www/images/timetree.png
inst/shinyWGD/www/images/ultrametricTree.Plot.svg
inst/shinyWGD/www/images/houseIcon.svg
inst/shinyWGD/www/images/timeTree.Plot.svg
inst/shinyWGD/www/images/treeReconciliationIcon.svg
inst/shinyWGD/www/images/logo_ugent.png
inst/shinyWGD/www/images/logo_ugent.svg
inst/shinyWGD/www/images/whale_hypothesis.speciesTree.svg
inst/shinyWGD/www/images/logo_lab.png
inst/shinyWGD/www/images/syntenyIcon.svg
inst/shinyWGD/www/images/code-solid.svg
inst/shinyWGD/www/images/pencil-solid.svg
inst/shinyWGD/www/images/ksIcon.svg
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/archive_compress_files_for_TreeRecon.shell
inst/shinyWGD/tools/running_diamond.shell
inst/shinyWGD/tools/archive_compress_files_for_visualization.shell
inst/shinyWGD/tools/obtain_newick_tree_from_timetree.R
inst/shinyWGD/tools/preparing_iadhore_inputs.shell
inst/shinyWGD/tools/run_paralog_ks_rest_species.sh
inst/shinyWGD/tools/cds2aa.R
inst/shinyWGD/tools/computing_Ks_tree_of_SingleCopyOrthologues.shell
inst/shinyWGD/tools/prepare_Whale_command.v2.sh
inst/shinyWGD/tools/computing_anchorpoint_ks.MultiThreads.shell
inst/shinyWGD/tools/rename_species.py
inst/shinyWGD/tools/preparing_Whale_inputs.shell
inst/shinyWGD/tools/prepare_orthofinder.R
inst/shinyWGD/tools/generating_iadhore_codes.local.shell
inst/shinyWGD/tools/Whale.jl/scripts/ccdfilter.py
inst/shinyWGD/tools/Whale.jl/scripts/tracer.py
inst/shinyWGD/tools/Whale.jl/scripts/orthofilter.py
inst/shinyWGD/tools/Whale.jl/scripts/ccddata.py
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
shinyWGD documentation built on April 4, 2025, 2:28 a.m.