2d71f213db5befe740ed081b1dbe41fc *DESCRIPTION
1d6660b90d74f8689a914ccbb8229ca8 *NAMESPACE
3ad46ae50f428b51cecf911acec85fda *NEWS.md
17ace9bcb5fc0e4c01561ba5dce3d1a1 *R/AddGenomeVectors.R
e205fbc86ceacf52821550be6d866920 *R/AnnotateResults.R
58099dec769df4f7837d4ec2e8bcdfd2 *R/CALANGO_brewer_pal.R
d5d963d4231843844196b357043baf64 *R/FileAddition.R
49d41487bebae8fc9ad7e824d72ff681 *R/FindContrasts.R
b07ccbc2f6a04584d17b6af485e42d76 *R/FindCorrelations.R
f4d0388802e3ae4fe7dc5ac7df5f7e6b *R/GenerateGenomeVector.R
9a4a1c8e783b3144cda35feda488cd65 *R/GenerateTree.R
ad0abb2c3094b15a243c40cf1775dac1 *R/GroupElementCount.R
694b26c8fe652793e300da0b3db18df7 *R/activate_CRAN_dependencies_from_Rmd_reports.R
f65f585f2bc8f10725f046e943ffe4b6 *R/check_bioc_dependencies.R
058ea7b3bcf0f5388fc17dda948f8280 *R/check_inputs_correlation.R
c1052c864ce85e9fabadcbf552a79473 *R/check_inputs_significance.R
49202016263ceeee17ff27a9398561d3 *R/clean_data.R
54daacd778540f3f925d564c49994386 *R/clean_data_correlation.R
97ae2ccaa37332dea35ae3ce7d9d39d1 *R/clean_data_significance.R
2d61a2f397c5ea32f1dcecb02a6eb4d8 *R/do_analysis.R
4019a0f8631e8dc0e3e9582e963eea47 *R/do_analysis_correlation.R
8aa2f306caeef6ec6e2667470544489e *R/do_analysis_significance.R
a0686d61574046bd27b33fa2685d19b6 *R/install_bioc_dependencies.R
3fdf199f0594ac3e2ffc1a9ec13e5cc8 *R/load_data.R
2d4b056a661b7d5f2078e54b94093309 *R/load_data_correlation.R
6c0b47a2bac0b36b0883172f0713892b *R/load_data_significance.R
32393071840fb5ce1f637b9a3b04aa0c *R/make_correlation_report.R
34a9cf9f859285616dbf00c081fa722a *R/make_report.R
4710c6f81c73b70a3b4380dce1ac9885 *R/make_significance_report.R
2d4cb67f17121e010df8fb18aa309828 *R/parse_GenomeMap.R
9acebb58a25a16b660a7b0eafb188dba *R/print_results_correlations.R
3f70af4ee7c18afd04fdffa4960f4286 *R/read_calango_file.R
0308efef5f4213c73332326b661f773f *R/restore_relative_paths.R
7f44c04144ddb04feb42ac9bf2541a7d *R/retrieve_calanguize_genomes.R
d989b36956d30e171974e9359789d202 *R/retrieve_data_files.R
af7462665db30ff1a30321abbef52c9d *R/run_CALANGO.R
03e5e44b91b5cf2f81c452ebc5af8975 *R/save_tsv_files.R
a9d19e63bb747a61ede707d35aea9f68 *R/set_absolute_paths.R
e038f1f8437ec74ab3cf68fa174f3259 *R/utils_ontology_manipulation.R
9f8f0b5e5823ff4fdaf4d839141feeed *README.md
fb09be99d3f3f3062e7bc2f299621b2b *build/vignette.rds
a12164a74a6db3609b3180fc659c2a33 *inst/CITATION
90eb32e48adb87489b26a8072071ac6f *inst/doc/CALANGO_Parameters.Rmd
bfdf200a7a23f0ef751c0f14e567a484 *inst/doc/CALANGO_Parameters.html
ad1db72916da20efc432f3f6d4e0aded *inst/extdata/calanguize_genomes.zip
0267251d31d86aa9e96a88e512f5a7bf *inst/extdata/report_files/_site.yml
55d785922a249ce931d03c393bc26ca3 *inst/extdata/report_files/about.Rmd
067e316c4a9de8afcf7098a199330448 *inst/extdata/report_files/heatmap_phylo_norm.Rmd
de8770fe4988e57ce76e2262319b002f *inst/extdata/report_files/heatmap_phylo_perc.Rmd
bac89b7f8c13f1e877f9cb24e8a3b662 *inst/extdata/report_files/heatmap_phylo_raw.Rmd
099b13f0aa6f743d06e0d2f59e641929 *inst/extdata/report_files/index.Rmd
4335ba569b81edd9e6160d4ce106489d *inst/extdata/report_files/q_value_scatter.Rmd
850926bfd34727941c230af44c6ff8a1 *inst/extdata/report_files/table.Rmd
da58948e64bc5ccc652f61b624023c74 *inst/images/CALANGO_LOGO_whiteBG.png
510c73684296acd702e880e4a389b5f9 *inst/images/CALANGO_interactive_table.png
0e1e1c8751e440d46200600d629ab5b6 *inst/images/KOMODO2_logo.png
c1589166c5777c6e71a048313aa0bc6c *inst/images/scatterplot_data.png
16f3a6604c457da292c2b0c25292b6fc *inst/images/scatterplot_phylogeny_aware_linear_model.png
45826b2ce7647038eb02ee1d556939e0 *inst/images/scatterplot_q_values.png
96ece070c933e6ed81f7e618acf41609 *inst/images/scatterplot_rank.png
ed04e087280f1f139691ce4df97eb41e *inst/scripts/count_GO_feature2GO.pl
84f8ac29a6d9b34d450a5334a5e21bad *inst/scripts/count_GO_gene2GO.pl
ef35c9a7bf6202ff9512e29bc8a7cc6a *inst/scripts/generate_symbolic_link.pl
12d13235fa02a69f2789369c2ebbf914 *inst/scripts/parse_busco.pl
c2a90b76980a1e5a181d3e8ef15f915b *inst/scripts/parse_interproscan_output.pl
41c1c70a50a2f62482883ed480afba6b *inst/scripts/parse_interproscan_output_IPR.pl
e98205d725832935674e3a7a4c43a51d *inst/scripts/parse_interproscan_output_feature2GO.pl
3cf89b08be1635272a41db0853d6d001 *inst/scripts/parse_interproscan_output_gene2GO.pl
8756a884d762ce0fff5ec11a460c4436 *inst/scripts/parse_interproscan_output_gene2SUPERFAMILY.pl
d2bc6b62d132e05df68b6bde7766f5b5 *man/install_bioc_dependencies.Rd
80e73003600984d3215b461162ed3b34 *man/make_report.Rd
fee9ad15b8dd0f5fad0f715908b51d26 *man/retrieve_calanguize_genomes.Rd
4b79e469ebe5c79a71a37b761a89f54e *man/retrieve_data_files.Rd
dd7aa156edd72b4e62083ecc4dcdf204 *man/run_CALANGO.Rd
90eb32e48adb87489b26a8072071ac6f *vignettes/CALANGO_Parameters.Rmd
