Files in mirnavazquez/RbiMs

R Tools for Reconstruncting Bin Metabolisms

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

R/CALC-calc_abundance.R R/CALC-calc_binary.R R/CALC-calc_percentage.R R/COLAPSE-read_interpro_colapsed.R R/GET-get_pca.R R/GET-get_subset_pathway.R R/GET-get_subset_pca.R R/GET-get_subseting_pathway.R R/GET-get_unique.R R/MAPPING-mapping_ko.R R/PLOT-bubble_dbcan.R R/PLOT-bubble_domain.R R/PLOT-bubble_ko.R R/PLOT-heatmap_dbcan.R R/PLOT-heatmap_domain.R R/PLOT-heatmap_ko.R R/PLOT-plot_bubble.R R/PLOT-plot_heatmap.R R/READ-read_dbCAN3.R R/READ-read_interpro.R R/READ-read_interpro_databases.R R/READ-read_ko.R R/READ-read_ko_shiny.R R/READ-read_picrust2.R R/SEPARATE-separate_kegg.R R/WRITE-write_metabolism.R R/data.R R/utils-pipe.R README.Rmd README.md

RbiMs.Rproj

_pkgdown.yml

data/.DS_Store

data/Rbims.RData

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/Create_Interpro_profile.html

docs/articles/Create_Interpro_profile_files/header-attrs-2.9/header-attrs.js

docs/articles/Create_KEGG_profile.html

docs/articles/Create_KEGG_profile_files/header-attrs-2.9/header-attrs.js

docs/articles/Explore_InterProScan_profile.html

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-14-1.png

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-19-1.png

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-19-2.png

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-5-1.png

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-6-1.png

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-7-1.png

docs/articles/Explore_InterProScan_profile_files/figure-html/unnamed-chunk-8-1.png

docs/articles/Explore_InterProScan_profile_files/header-attrs-2.9/header-attrs.js

docs/articles/Explore_KEGG_profile.html

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-11-1.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-15-1.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-15-2.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-19-1.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-19-2.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-20-1.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-20-2.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-21-1.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-21-2.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-22-1.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-22-2.png

docs/articles/Explore_KEGG_profile_files/figure-html/unnamed-chunk-9-1.png

docs/articles/Explore_KEGG_profile_files/header-attrs-2.9/header-attrs.js

docs/articles/Installation.html

docs/articles/Installation_files/header-attrs-2.9/header-attrs.js

docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/calc_binary.html

docs/reference/calc_percentage.html

docs/reference/figures/Logo-rRbiMs.png

docs/reference/figures/rRbiMs-3.png

docs/reference/get_subset_pathway.html

docs/reference/get_subset_pca.html

docs/reference/get_subset_unique.html

docs/reference/index.html

docs/reference/interpro_INTERPRO_long.html

docs/reference/interpro_INTERPRO_profile.html

docs/reference/interpro_KEGG_long.html

docs/reference/interpro_map.html

docs/reference/interpro_pfam_long.html

docs/reference/interpro_pfam_profile.html

docs/reference/ko_bin_mapp.html

docs/reference/ko_bin_table.html

docs/reference/mapping_ko.html

docs/reference/metadata.html

docs/reference/pipe.html

docs/reference/plot_bubble-1.png

docs/reference/plot_bubble.html

docs/reference/plot_heatmap.html

docs/reference/rbims.html

docs/reference/read_interpro.html

docs/reference/read_ko.html

inst/.DS_Store

inst/Example_bubble.png

inst/Example_bubble_order.png

inst/WORDLIST

inst/example_heatmap.png

inst/extdata/.DS_Store

inst/extdata/Interpro_test.tsv

inst/extdata/KEGG_bins.txt

inst/extdata/metadata.xlsx

inst/extdata/pred_metagenome_unstrat.tsv

inst/extdata/test_data/104_overview.txt

inst/extdata/test_data/108_overview.txt

inst/rRbiMs-3.png

man/.DS_Store

man/calc_binary.Rd man/calc_percentage.Rd

man/figures/Logo-rRbiMs.png

man/figures/rRbiMs-3.png

man/get_subset_pathway.Rd man/get_subset_pca.Rd man/get_subset_unique.Rd man/interpro_INTERPRO_long.Rd man/interpro_INTERPRO_profile.Rd man/interpro_KEGG_long.Rd man/interpro_map.Rd man/interpro_pfam_long.Rd man/interpro_pfam_profile.Rd man/ko_bin_mapp.Rd man/ko_bin_table.Rd man/mapping_ko.Rd man/metadata.Rd man/pipe.Rd man/plot_bubble.Rd man/plot_heatmap.Rd

man/rRbiMs-3.png

man/rbims.Rd man/read_dbcan3.Rd man/read_interpro.Rd man/read_ko.Rd man/read_ko_shiny.Rd man/read_picrust2.Rd man/write_metabolism.Rd tests/testthat.R tests/testthat/test-plot-bubble.R tests/testthat/test-read_interpro.R

vignettes/.DS_Store

vignettes/.gitignore

vignettes/Create_Interpro_profile.Rmd vignettes/Create_KEGG_profile.Rmd vignettes/Explore_InterProScan_profile.Rmd vignettes/Explore_KEGG_profile.Rmd vignettes/Installation.Rmd

vignettes/Interpro.tsv

vignettes/KEGG_mapped.tsv

mirnavazquez/RbiMs documentation built on March 6, 2024, 10:27 p.m.