Files in fcampelo/KOMODO2-CRAN
Kegg Orthology EnrichMent Online DetectiOn
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
KOMODO2.Rproj
LICENSE
NAMESPACE
NEWS.md
R/AddGenomeVectors.R
R/FindContrasts.R
R/FindCorrelations.R
R/check_inputs_correlation.R
R/check_inputs_significance.R
R/clean_data.R
R/clean_data_correlation.R
R/clean_data_significance.R
R/do_analysis.R
R/do_analysis_correlation.R
R/load_data.R
R/load_data_correlation.R
R/load_data_significance.R
R/make_correlation_report.R
R/print_c_results.R
R/run_KOMODO2.R
R/save_tsv_files.R
R/utils_general.R
R/utils_genome_vector.R
R/utils_ontology_manipulation.R
README.md
cran-comments.md
inst/extdata/KOMODO2_correlation_report.Rmd
inst/extdata/Pfam/GCA_000004555
inst/extdata/Pfam/GCA_000004555.3.Pfam.txt
inst/extdata/Pfam/GCA_000180735
inst/extdata/Pfam/GCA_000180735.1.Pfam.txt
inst/extdata/Pfam/GCA_000187875
inst/extdata/Pfam/GCA_000187875.1.Pfam.txt
inst/extdata/Pfam/GCA_002081595
inst/extdata/Pfam/GCA_002081595.1.Pfam.txt
inst/extdata/Pfam/GCF_000001215
inst/extdata/Pfam/GCF_000001215.4.Pfam.txt
inst/extdata/Pfam/GCF_000001405
inst/extdata/Pfam/GCF_000001405.37.Pfam.txt
inst/extdata/Pfam/GCF_000001635
inst/extdata/Pfam/GCF_000001635.26.Pfam.txt
inst/extdata/Pfam/GCF_000001735
inst/extdata/Pfam/GCF_000001735.3.Pfam.txt
inst/extdata/Pfam/GCF_000001895
inst/extdata/Pfam/GCF_000001895.5.Pfam.txt
inst/extdata/Pfam/GCF_000002035
inst/extdata/Pfam/GCF_000002035.6.Pfam.txt
inst/extdata/Pfam/GCF_000002285
inst/extdata/Pfam/GCF_000002285.3.Pfam.txt
inst/extdata/Pfam/GCF_000002315
inst/extdata/Pfam/GCF_000002315.6.Pfam.txt
inst/extdata/Pfam/GCF_000002515
inst/extdata/Pfam/GCF_000002515.2.Pfam.txt
inst/extdata/Pfam/GCF_000002595
inst/extdata/Pfam/GCF_000002595.1.Pfam.txt
inst/extdata/Pfam/GCF_000002945
inst/extdata/Pfam/GCF_000002945.1.Pfam.txt
inst/extdata/Pfam/GCF_000002985
inst/extdata/Pfam/GCF_000002985.6.Pfam.txt
inst/extdata/Pfam/GCF_000003195
inst/extdata/Pfam/GCF_000003195.3.Pfam.txt
inst/extdata/Pfam/GCF_000003745
inst/extdata/Pfam/GCF_000003745.3.Pfam.txt
inst/extdata/Pfam/GCF_000003815
inst/extdata/Pfam/GCF_000003815.1.Pfam.txt
inst/extdata/Pfam/GCF_000004095
inst/extdata/Pfam/GCF_000004095.1.Pfam.txt
inst/extdata/Pfam/GCF_000004195
inst/extdata/Pfam/GCF_000004195.3.Pfam.txt
inst/extdata/Pfam/GCF_000004695
inst/extdata/Pfam/GCF_000004695.1.Pfam.txt
inst/extdata/Pfam/GCF_000005425
inst/extdata/Pfam/GCF_000005425.2.Pfam.txt
inst/extdata/Pfam/GCF_000005505
inst/extdata/Pfam/GCF_000005505.3.Pfam.txt
inst/extdata/Pfam/GCF_000005575
inst/extdata/Pfam/GCF_000005575.2.Pfam.txt
inst/extdata/Pfam/GCF_000090745
inst/extdata/Pfam/GCF_000090745.1.Pfam.txt
inst/extdata/Pfam/GCF_000090795
inst/extdata/Pfam/GCF_000090795.1.Pfam.txt
inst/extdata/Pfam/GCF_000142945
inst/extdata/Pfam/GCF_000142945.1.Pfam.txt
inst/extdata/Pfam/GCF_000143455
inst/extdata/Pfam/GCF_000143455.1.Pfam.txt
inst/extdata/Pfam/GCF_000146045
inst/extdata/Pfam/GCF_000146045.2.Pfam.txt
inst/extdata/Pfam/GCF_000149205
inst/extdata/Pfam/GCF_000149205.2.Pfam.txt
inst/extdata/Pfam/GCF_000149755
inst/extdata/Pfam/GCF_000149755.1.Pfam.txt
inst/extdata/Pfam/GCF_000150275
inst/extdata/Pfam/GCF_000150275.1.Pfam.txt
inst/extdata/Pfam/GCF_000151315
inst/extdata/Pfam/GCF_000151315.2.Pfam.txt
inst/extdata/Pfam/GCF_000151545
inst/extdata/Pfam/GCF_000151545.1.Pfam.txt
inst/extdata/Pfam/GCF_000181335
inst/extdata/Pfam/GCF_000181335.3.Pfam.txt
inst/extdata/Pfam/GCF_000182925
inst/extdata/Pfam/GCF_000182925.2.Pfam.txt
inst/extdata/Pfam/GCF_000209225
inst/extdata/Pfam/GCF_000209225.1.Pfam.txt
inst/extdata/Pfam/GCF_000214015
inst/extdata/Pfam/GCF_000214015.3.Pfam.txt
inst/extdata/Pfam/GCF_000224145
inst/extdata/Pfam/GCF_000224145.3.Pfam.txt
inst/extdata/Pfam/GCF_000247585
inst/extdata/Pfam/GCF_000247585.1.Pfam.txt
inst/extdata/Pfam/GCF_000328475
inst/extdata/Pfam/GCF_000328475.2.Pfam.txt
inst/extdata/Pfam/GCF_002263795
inst/extdata/Pfam/GCF_002263795.1.Pfam.txt
inst/extdata/Pfam/GCF_002880755
inst/extdata/Pfam/GCF_002880755.1.Pfam.txt
inst/extdata/Pfam/GCF_003254395
inst/extdata/Pfam/GCF_003254395.2.Pfam.txt
inst/extdata/Pfam/GCF_901000725
inst/extdata/Pfam/GCF_901000725.2.Pfam.txt
inst/extdata/dics/Pfam.dic
inst/extdata/dics/Pfam_less_H_sapiens.dic
inst/extdata/gene2GO/GCA_000004555
inst/extdata/gene2GO/GCA_000004555.3.gene2GO.txt
inst/extdata/gene2GO/GCA_000180735
inst/extdata/gene2GO/GCA_000180735.1.gene2GO.txt
inst/extdata/gene2GO/GCA_000187875
inst/extdata/gene2GO/GCA_000187875.1.gene2GO.txt
inst/extdata/gene2GO/GCA_002081595
inst/extdata/gene2GO/GCA_002081595.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000001215
inst/extdata/gene2GO/GCF_000001215.4.gene2GO.txt
inst/extdata/gene2GO/GCF_000001405
inst/extdata/gene2GO/GCF_000001405.37.gene2GO.txt
inst/extdata/gene2GO/GCF_000001635
inst/extdata/gene2GO/GCF_000001635.26.gene2GO.txt
inst/extdata/gene2GO/GCF_000001735
inst/extdata/gene2GO/GCF_000001735.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000001895
inst/extdata/gene2GO/GCF_000001895.5.gene2GO.txt
inst/extdata/gene2GO/GCF_000002035
inst/extdata/gene2GO/GCF_000002035.6.gene2GO.txt
inst/extdata/gene2GO/GCF_000002285
inst/extdata/gene2GO/GCF_000002285.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000002315
inst/extdata/gene2GO/GCF_000002315.6.gene2GO.txt
inst/extdata/gene2GO/GCF_000002515
inst/extdata/gene2GO/GCF_000002515.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000002595
inst/extdata/gene2GO/GCF_000002595.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000002945
inst/extdata/gene2GO/GCF_000002945.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000002985
inst/extdata/gene2GO/GCF_000002985.6.gene2GO.txt
inst/extdata/gene2GO/GCF_000003195
inst/extdata/gene2GO/GCF_000003195.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000003745
inst/extdata/gene2GO/GCF_000003745.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000003815
inst/extdata/gene2GO/GCF_000003815.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000004095
inst/extdata/gene2GO/GCF_000004095.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000004195
inst/extdata/gene2GO/GCF_000004195.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000004695
inst/extdata/gene2GO/GCF_000004695.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000005425
inst/extdata/gene2GO/GCF_000005425.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000005505
inst/extdata/gene2GO/GCF_000005505.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000005575
inst/extdata/gene2GO/GCF_000005575.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000090745
inst/extdata/gene2GO/GCF_000090745.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000090795
inst/extdata/gene2GO/GCF_000090795.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000142945
inst/extdata/gene2GO/GCF_000142945.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000143455
inst/extdata/gene2GO/GCF_000143455.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000146045
inst/extdata/gene2GO/GCF_000146045.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000149205
inst/extdata/gene2GO/GCF_000149205.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000149755
inst/extdata/gene2GO/GCF_000149755.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000150275
inst/extdata/gene2GO/GCF_000150275.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000151315
inst/extdata/gene2GO/GCF_000151315.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000151545
inst/extdata/gene2GO/GCF_000151545.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000181335
inst/extdata/gene2GO/GCF_000181335.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000182925
inst/extdata/gene2GO/GCF_000182925.2.gene2GO.txt
inst/extdata/gene2GO/GCF_000209225
inst/extdata/gene2GO/GCF_000209225.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000214015
inst/extdata/gene2GO/GCF_000214015.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000224145
inst/extdata/gene2GO/GCF_000224145.3.gene2GO.txt
inst/extdata/gene2GO/GCF_000247585
inst/extdata/gene2GO/GCF_000247585.1.gene2GO.txt
inst/extdata/gene2GO/GCF_000328475
inst/extdata/gene2GO/GCF_000328475.2.gene2GO.txt
inst/extdata/gene2GO/GCF_002263795
inst/extdata/gene2GO/GCF_002263795.1.gene2GO.txt
inst/extdata/gene2GO/GCF_002880755
inst/extdata/gene2GO/GCF_002880755.1.gene2GO.txt
inst/extdata/gene2GO/GCF_003254395
inst/extdata/gene2GO/GCF_003254395.2.gene2GO.txt
inst/extdata/gene2GO/GCF_901000725
inst/extdata/gene2GO/GCF_901000725.2.gene2GO.txt
inst/extdata/metadata/GO_metadata_Pan_proxy.txt
inst/extdata/metadata/GO_metadata_less_H_sapiens.txt
inst/extdata/metadata/GO_metadata_standard.txt
inst/extdata/metadata/Pfam_metadata_Pan_proxy.txt
inst/extdata/metadata/Pfam_metadata_less_H_sapiens.txt
inst/extdata/metadata/Pfam_metadata_standard.txt
inst/extdata/sample_parameter_files/parameters_Pfam_Pan_proxy.R
inst/extdata/sample_parameter_files/parameters_gene2GO_Pan_proxy.R
inst/extdata/sample_parameter_files/parameters_gene2GO_Pan_proxy.txt
inst/extdata/sample_parameter_files/parameters_validation/parameters_Pfam_Pan_proxy.R
inst/extdata/sample_parameter_files/parameters_validation/parameters_Pfam_less_H_sapiens.R
inst/extdata/sample_parameter_files/parameters_validation/parameters_Pfam_standard.R
inst/extdata/sample_parameter_files/parameters_validation/parameters_gene2GO_Pan_proxy.R
inst/extdata/sample_parameter_files/parameters_validation/parameters_gene2GO_less_H_sapiens.R
inst/extdata/sample_parameter_files/parameters_validation/parameters_gene2GO_standard.R
inst/extdata/test_defs.rds
inst/extdata/trees/tree_genome_IDs.nwk
inst/extdata/trees/tree_genome_IDs_less_H_sapiens.nwk
inst/scripts/count_GO_feature2GO.pl
inst/scripts/count_GO_gene2GO.pl
inst/scripts/generate_symbolic_link.pl
inst/scripts/parse_busco.pl
inst/scripts/parse_interproscan_output.pl
inst/scripts/parse_interproscan_output_IPR.pl
inst/scripts/parse_interproscan_output_feature2GO.pl
inst/scripts/parse_interproscan_output_gene2GO.pl
inst/scripts/parse_interproscan_output_gene2SUPERFAMILY.pl
man/AddGenomeVectors.Rd
man/clean_data.Rd
man/do_analysis.Rd
man/do_analysis_correlation.Rd
man/load_data.Rd
man/run_KOMODO2.Rd
results/GO_Pan_proxy/KOMODO2_report.html
results/GO_Pan_proxy/contrasts_corrected.tsv
results/GO_Pan_proxy/contrasts_raw.tsv
results/GO_Pan_proxy/correlation_Plots/GO:0000003.html
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