Files in trvinh/test

PhyloProfile

.Rbuildignore

.gitignore

.travis.yml

CODE_OF_CONDUCT.md CONTRIBUTING.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/analyze_distribution.R R/cluster_profile.R R/compare_taxa_groups.R R/create_color_scheme.R R/create_domain_plot.R R/create_profile_plot.R R/create_taxonomy_matrix.R R/data.R R/estimate_gene_age.R R/get_fasta_seqs.R R/get_oma_browser.R R/identify_core_gene.R R/parse_domain_input.R R/parse_main_input.R R/parse_phylo_profile.R R/parse_phylotree.R R/run_phyloprofile.R R/search_taxon_id.R README.md

_config.yml

data/full_processed_profile.RData

data/full_processed_profile_large.RData

data/main_long_raw.RData

data/pp_taxonomy_matrix.RData

data/pp_tree.RData

data/profile_with_taxonomy.RData

inst/CITATION

inst/extdata/README.md

inst/extdata/data/idList.txt

inst/extdata/data/rankList.txt

inst/extdata/data/taxonNamesFull.txt

inst/extdata/domain_files/OG_1009.domains

inst/extdata/domain_files/OG_1017.domains

inst/extdata/domain_files/OG_1019.domains

inst/extdata/domain_files/OG_1020.domains

inst/extdata/domain_files/OG_1023.domains

inst/extdata/domain_files/OG_1024.domains

inst/extdata/domain_files/OG_1026.domains

inst/extdata/domain_files/OG_1027.domains

inst/extdata/domain_files/OG_1029.domains

inst/extdata/domain_files/OG_1030.domains

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/[e-mail]

inst/extdata/fasta_files/concatenatedFile.fa

inst/extdata/oma/omaIDs.list

inst/extdata/oma/oma_example.orthoxml

inst/extdata/oma/oma_example_phyloprofile_compatible.orthoxml

inst/extdata/oma/taxon_mapping_oma_orthoxml.csv

inst/extdata/others/test.geneList

inst/extdata/others/test.taxaList

inst/extdata/pfamAnno/hmmscanOut.txt

inst/extdata/pfamAnno/hmmscanOut.txt.domains

inst/extdata/pfamAnno/pfamscanOut.txt

inst/extdata/pfamAnno/pfamscanOut.txt.domains

inst/extdata/test.main.fasta

inst/extdata/test.main.long

inst/extdata/test.main.wide

inst/extdata/test.main.xml

inst/phyloprofile/R/analyze_distribution.R inst/phyloprofile/R/cluster_profile.R inst/phyloprofile/R/create_architecture_plot.R inst/phyloprofile/R/create_detailed_plot.R inst/phyloprofile/R/create_profile_plot.R inst/phyloprofile/R/download_filtered_customized.R inst/phyloprofile/R/download_filtered_main.R inst/phyloprofile/R/estimate_gene_age.R inst/phyloprofile/R/functions.R inst/phyloprofile/R/group_comparison.R inst/phyloprofile/R/identify_core_gene.R inst/phyloprofile/R/search_taxon_id.R inst/phyloprofile/R/select_taxon_rank.R inst/phyloprofile/global.R

inst/phyloprofile/help.html

inst/phyloprofile/scripts/convert_oma_standalone_orthoxml.py

inst/phyloprofile/scripts/fastaParser.py

inst/phyloprofile/scripts/get_oma_browser.py

inst/phyloprofile/scripts/hmmscanParser.py

inst/phyloprofile/scripts/ncbi_taxonomy_parser.py

inst/phyloprofile/scripts/orthoxmlParser.py

inst/phyloprofile/scripts/pfamscanParser.py

inst/phyloprofile/server.R inst/phyloprofile/ui.R man/calc_pres_spec.Rd man/calculate_p_value.Rd man/check_input_validity.Rd man/check_newick.Rd man/check_oma_id.Rd man/cluster_data_dend.Rd man/create_archi_plot.Rd man/create_domain_df.Rd man/create_gene_age_plot.Rd man/create_long_matrix.Rd man/create_percentage_distribution_data.Rd man/create_profile_data.Rd man/create_profile_from_oma.Rd man/create_rooted_tree.Rd man/create_var_dist_plot.Rd man/create_variable_distribution_data.Rd man/create_variable_distribution_data_subset.Rd man/data_customized_plot.Rd man/data_main_plot.Rd man/domain_plotting.Rd man/estimate_gene_age.Rd man/fasta_parser.Rd man/from_input_to_profile.Rd man/full_processed_profile.Rd man/full_processed_profile_large.Rd man/gene_age_plotDf.Rd man/get_all_domains_oma.Rd man/get_all_fasta_oma.Rd man/get_common_ancestor.Rd man/get_core_gene.Rd man/get_data_clustering.Rd man/get_data_for_one_oma.Rd man/get_data_for_one_ortholog.Rd man/get_dendrogram.Rd man/get_distance_matrix.Rd man/get_domain_file.Rd man/get_domain_folder.Rd man/get_domain_from_url.Rd man/get_domain_online.Rd man/get_fasta_seqs.Rd man/get_features.Rd man/get_ids_rank.Rd man/get_input_taxa_id.Rd man/get_input_taxa_name.Rd man/get_name_list.Rd man/get_oma_members.Rd man/get_p_values.Rd man/get_prefix_features.Rd man/get_qual_col_for_vector.Rd man/get_selected_fasta_oma.Rd man/get_selected_subset.Rd man/get_significant_genes.Rd man/get_taxonomy_matrix.Rd man/get_taxonomy_ranks.Rd man/heatmap_plotting.Rd man/highlight_profile_plot.Rd man/main_long_raw.Rd man/parse_domain_input.Rd man/parse_info_profile.Rd man/pp_taxonomy_matrix.Rd man/pp_tree.Rd man/profile_with_taxonomy.Rd man/qualitative_colours.Rd man/rankIndexing.Rd man/reduce_profile.Rd man/run_phyloprofile.Rd man/search_taxonID_online.Rd man/sort_domains.Rd man/sort_input_taxa.Rd man/sort_taxa_from_tree.Rd man/str_reverse.Rd man/taxa2dist.Rd man/taxa_select_gc.Rd man/taxonomy_table_creator.Rd man/wide_to_long.Rd man/xml_parser.Rd tests/testthat.R

tests/testthat/domains/OG_1029.domains

tests/testthat/idList_test.txt

tests/testthat/main_fasta_test.txt

tests/testthat/main_orthoxml_test.xml

tests/testthat/main_wide_test.txt

tests/testthat/rankList_test.txt

tests/testthat/taxonNames_test.txt

tests/testthat/taxonomyMatrix_test.txt

tests/testthat/test_OMAparser.R tests/testthat/test_createDataProfilePlot.R tests/testthat/test_createDistributionPlot.R tests/testthat/test_createDomainPlot.R tests/testthat/test_createTaxonomyMatrix.R tests/testthat/test_estimateGeneAge.R tests/testthat/test_identifyCoreGene.R tests/testthat/test_parseDomainInput.R tests/testthat/test_parseMainInput.R tests/testthat/test_parsePhyloProfile.R tests/testthat/test_searchTaxonID.R vignettes/phyloprofile-vignette.Rmd

vignettes/poster.png

www/blank.jpg

www/pic_customized.png

www/pic_input.png

www/pic_main.png

www/pic_taxaIDsearch.png

www/poster.png

www/posterSub.png

www/spinner.gif

trvinh/test documentation built on May 9, 2019, 2:26 a.m.