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/A.fabrum@176299.fa
inst/extdata/fasta_files/A.pernix@272557.fa
inst/extdata/fasta_files/A.thaliana@3702.fa
inst/extdata/fasta_files/E.intestinalis@876142.fa
inst/extdata/fasta_files/H.sapiens@9606.fa
inst/extdata/fasta_files/M.musculus@10090.fa
inst/extdata/fasta_files/N.parisii@586133.fa
inst/extdata/fasta_files/P.blakesleeanus@4837.fa
inst/extdata/fasta_files/S.lycopersicum@4081.fa
inst/extdata/fasta_files/S.purpuratus@7668.fa
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
