e04e8b4513f7c3f32e6a67c283d19a41 *DESCRIPTION
6239afc49b3411cc53124a04c8ad9f29 *NAMESPACE
1ebf7ed4a9ce54c7cf4723e424d00847 *NEWS.md
57b2b016ac9427dd257e93258ae74bff *R/AddGenomeVectors.R
893030f4cd9ae1643be3a49a605fec24 *R/AnnotateResults.R
58a5adfa20229d79101c5e7a33cb5609 *R/CALANGO_brewer_pal.R
d03017ac5b3bd225b2ddbf6a344e2ecb *R/FileAddition.R
11bf64b990d6ae0e0b4fd3633f8b53e9 *R/FindContrasts.R
583451e0a6db9c547fdbb81716ef6eeb *R/FindCorrelations.R
2d6a94129da5c8c628b1bd85e973b715 *R/GenerateGenomeVector.R
c38009fa99bf78567a099db0bef143d3 *R/GenerateTree.R
57c1d634336ecad7d0a0753e267035f0 *R/GroupElementCount.R
c4ec4d3fa93de3dc7804894b87cdc3f2 *R/activate_CRAN_dependencies_from_Rmd_reports.R
e26a3b5f4e410c42b41a4f211e80d67c *R/check_bioc_dependencies.R
2febea5551c31e2edd44ce56eb656e7b *R/check_inputs_correlation.R
bc2f0ec6d4038fb65d2065dbd4c9c6f0 *R/check_inputs_significance.R
77af0b63c414b8b6aed2953d0e1ac1b4 *R/clean_data.R
3b090c7338f5de26a2fbf9a916e000c0 *R/clean_data_correlation.R
f5e6b297f3f83b414d45508edfe1f770 *R/clean_data_significance.R
b312a62ea15a65ff11c5cef7eba57bc3 *R/do_analysis.R
041ea027f7cab3ae7bf082f37fd3ffbc *R/do_analysis_correlation.R
038c3941b138a7d07bbf923246be7f17 *R/do_analysis_significance.R
2c5172f22c903bb62c157f63573b662c *R/install_bioc_dependencies.R
b3373f3e7927725eb08cd1ff35381a95 *R/load_data.R
e6cbbb58cadf45663d020e75953e7c88 *R/load_data_correlation.R
6c00984b1641b4ec51e5ec4a3f329c79 *R/load_data_significance.R
cf42dcaf1e54c27ac22be467010a88c7 *R/make_correlation_report.R
d53a2211225fb51555ca6b9a05ceea16 *R/make_report.R
b64f6dc2548e8a47b307a3afe6cb0a68 *R/make_significance_report.R
dff6e3efa9921f21451d2678d0699be7 *R/parse_GenomeMap.R
8e06847e3042c8039a78730f8e53294a *R/print_results_correlations.R
efebf6e05a1f95e7ed226f5965dd31b3 *R/read_calango_file.R
f8f4d3b6a63cd2fc337bcc7b587c8bad *R/restore_relative_paths.R
0d8296fb556596377d764c2b22da3dff *R/retrieve_calanguize_genomes.R
9a64c6d4c8494b2d2f47d2082e183dac *R/retrieve_data_files.R
4c7b42177ea4ca7f4af166b1d142a928 *R/run_CALANGO.R
6e046173b9aaaabd811a0b4d58c6bf25 *R/save_tsv_files.R
a78ca58b494a6441fa36735a4793d1e0 *R/set_absolute_paths.R
eda0bfdccfeeb86041994b56b2969bb0 *R/utils_ontology_manipulation.R
8524a4857c624e2914d60c2cb05fe92e *README.md
20b93d11fd5a7689340c03132d2cb488 *build/vignette.rds
bdb554b44fa78aca02ace80c2cee47e6 *inst/CITATION
5e8b0054c466627d3ca1b865f74151c7 *inst/doc/CALANGO_Parameters.Rmd
f95978e5ed91f9f26d6ba8d1db5c1123 *inst/doc/CALANGO_Parameters.html
ad1db72916da20efc432f3f6d4e0aded *inst/extdata/calanguize_genomes.zip
7cf3334542011a68d34cb00b4a205977 *inst/extdata/report_files/_site.yml
593a442752b361072e89a18e803033d6 *inst/extdata/report_files/about.Rmd
8db1bbefb39f208e842481c0b39879d2 *inst/extdata/report_files/heatmap_phylo_norm.Rmd
63cac7fb115c58ef901952f8111cad8d *inst/extdata/report_files/heatmap_phylo_perc.Rmd
b4443c537f270e5dbcf0b787f2533fa8 *inst/extdata/report_files/heatmap_phylo_raw.Rmd
4440ec09cbe7c5014ca1df516a3ce85c *inst/extdata/report_files/index.Rmd
b1367989cf2e4679f9adb4a8c18f98a0 *inst/extdata/report_files/q_value_scatter.Rmd
ccbb30f95a8b3cd6420337e512b56f68 *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
4e84d7c15bdbfac6b559b4765f31e100 *inst/scripts/count_GO_feature2GO.pl
296d2d564adf5384da2b5f7e45a5e9ce *inst/scripts/count_GO_gene2GO.pl
ccd8524023fbdf842517f3f37241fc4c *inst/scripts/generate_symbolic_link.pl
8427c6dbd7b5fa9472308b101bf44633 *inst/scripts/parse_busco.pl
dbd07c4b51b1a30a20aac19831305d61 *inst/scripts/parse_interproscan_output.pl
1eb94772b2fd8f0c1c95f3f2ef1ae231 *inst/scripts/parse_interproscan_output_IPR.pl
56f73b38af07b49319480267a594f729 *inst/scripts/parse_interproscan_output_feature2GO.pl
4ea481db8a154c245d607436fad1c25b *inst/scripts/parse_interproscan_output_gene2GO.pl
c638a8ecc76f37d0b18575090558a190 *inst/scripts/parse_interproscan_output_gene2SUPERFAMILY.pl
6f1bc749eb965c4bcfb22c56163d5fbb *man/install_bioc_dependencies.Rd
1c0b1b4d327e8fea3098a47c7489866a *man/make_report.Rd
47e1cbd7f48ed190557cb374930fa88e *man/retrieve_calanguize_genomes.Rd
2aaaae2c8a823e8c6f362cf48771b01b *man/retrieve_data_files.Rd
7ffd999f9f0253f5f3ed1f20ecc25d79 *man/run_CALANGO.Rd
5e8b0054c466627d3ca1b865f74151c7 *vignettes/CALANGO_Parameters.Rmd
