OceaneCsn/DIANE
DIANE

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DIANE

.Rbuildignore
.github/.gitignore
.gitignore
.travis.yml
CITATION.cff
DESCRIPTION
Dockerfile
LICENSE.md
NAMESPACE
R/abiotic_stresses.R R/app_config.R R/app_server.R R/app_ui.R R/fct_GENIE3_oob.R R/fct_coseq.R R/fct_dea.R R/fct_edge_testing.R R/fct_geneIDs.R R/fct_glm.R R/fct_go.R R/fct_network_analysis.R R/fct_network_inference.R R/fct_normalisation.R R/fct_regressors_grouping.R R/fct_viz.R R/gene_annotations.R R/golem_utils_server.R R/golem_utils_ui.R R/mod_cluster_exploration.R R/mod_clustering.R R/mod_context.R R/mod_datasets.R R/mod_differential_expression_analysis.R R/mod_import_data.R R/mod_legal_mentions.R R/mod_module_levels.R R/mod_network_analysis.R R/mod_network_inference.R R/mod_normalisation.R R/mod_versions.R R/regulators_per_organism.R R/run_app.R
R/sysdata.rda
README.md
_pkgdown.yml
app.R
data/abiotic_stresses.rda
data/gene_annotations.rda
data/go_matchings.rda
data/regulators_per_organism.rda
dev/01_start.R dev/02_dev.R dev/03_deploy.R dev/examples.R dev/random_seed.R dev/reactiveValues.md dev/run_dev.R
docs/404.html
docs/LICENSE.html
docs/articles/DIANE.html
docs/articles/DIANE_Input_data.html
docs/articles/DIANE_Input_data_files/anchor-sections-1.0/anchor-sections.css
docs/articles/DIANE_Input_data_files/anchor-sections-1.0/anchor-sections.js
docs/articles/DIANE_Input_data_files/header-attrs-2.4.6/header-attrs.js
docs/articles/DIANE_Programming_Interface.html
docs/articles/DIANE_Programming_Interface_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/DIANE_Programming_Interface_files/anchor-sections-1.0/anchor-sections.css
docs/articles/DIANE_Programming_Interface_files/anchor-sections-1.0/anchor-sections.js
docs/articles/DIANE_Programming_Interface_files/crosstalk-1.1.0.1/css/crosstalk.css
docs/articles/DIANE_Programming_Interface_files/crosstalk-1.1.0.1/js/crosstalk.js
docs/articles/DIANE_Programming_Interface_files/crosstalk-1.1.0.1/js/crosstalk.js.map
docs/articles/DIANE_Programming_Interface_files/crosstalk-1.1.0.1/js/crosstalk.min.js
docs/articles/DIANE_Programming_Interface_files/crosstalk-1.1.0.1/js/crosstalk.min.js.map
docs/articles/DIANE_Programming_Interface_files/figure-html/communities-2.png
docs/articles/DIANE_Programming_Interface_files/figure-html/communities-3.png
docs/articles/DIANE_Programming_Interface_files/figure-html/communities-4.png
docs/articles/DIANE_Programming_Interface_files/figure-html/coseq-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/coseq-2.png
docs/articles/DIANE_Programming_Interface_files/figure-html/dea-1.png
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docs/articles/DIANE_Programming_Interface_files/figure-html/dea-3.png
docs/articles/DIANE_Programming_Interface_files/figure-html/dea-4.png
docs/articles/DIANE_Programming_Interface_files/figure-html/genie3-2.png
docs/articles/DIANE_Programming_Interface_files/figure-html/glm-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/go_enrich-2.png
docs/articles/DIANE_Programming_Interface_files/figure-html/levels-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/mds-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/normalize-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/pca-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/profiles-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/profiles-2.png
docs/articles/DIANE_Programming_Interface_files/figure-html/testing-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/unnamed-chunk-3-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/unnamed-chunk-3-2.png
docs/articles/DIANE_Programming_Interface_files/figure-html/unnamed-chunk-4-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/venn-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/vis_raw-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/viz_filter-1.png
docs/articles/DIANE_Programming_Interface_files/figure-html/viz_filter-2.png
docs/articles/DIANE_Programming_Interface_files/header-attrs-2.4.6/header-attrs.js
docs/articles/DIANE_Programming_Interface_files/htmlwidgets-1.5.1/htmlwidgets.js
docs/articles/DIANE_Programming_Interface_files/htmlwidgets-1.5.2/htmlwidgets.js
docs/articles/DIANE_Programming_Interface_files/jquery-1.11.3/jquery-AUTHORS.txt
docs/articles/DIANE_Programming_Interface_files/jquery-1.11.3/jquery.js
docs/articles/DIANE_Programming_Interface_files/jquery-1.11.3/jquery.min.js
docs/articles/DIANE_Programming_Interface_files/jquery-1.11.3/jquery.min.map
docs/articles/DIANE_Programming_Interface_files/plotly-binding-4.9.2.1/plotly.js
docs/articles/DIANE_Programming_Interface_files/plotly-htmlwidgets-css-1.52.2/plotly-htmlwidgets.css
docs/articles/DIANE_Programming_Interface_files/plotly-main-1.52.2/plotly-latest.min.js
docs/articles/DIANE_Programming_Interface_files/typedarray-0.1/typedarray.min.js
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/acceptDeleteIcon.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/addNodeIcon.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/backIcon.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/connectIcon.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/cross.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/cross2.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/deleteIcon.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/downArrow.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/editIcon.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/leftArrow.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/minus.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/plus.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/rightArrow.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/upArrow.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/img/network/zoomExtends.png
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/vis.css
docs/articles/DIANE_Programming_Interface_files/vis-4.20.1/vis.min.js
docs/articles/DIANE_Programming_Interface_files/visNetwork-binding-2.0.9/visNetwork.js
docs/articles/DIANE_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/DIANE_files/anchor-sections-1.0/anchor-sections.css
docs/articles/DIANE_files/anchor-sections-1.0/anchor-sections.js
docs/articles/DIANE_files/header-attrs-2.4.6/header-attrs.js
docs/articles/DIANE_normalize.html
docs/articles/DIANE_normalize_files/anchor-sections-1.0/anchor-sections.css
docs/articles/DIANE_normalize_files/anchor-sections-1.0/anchor-sections.js
docs/articles/DIANE_normalize_files/header-attrs-2.4.6/header-attrs.js
docs/articles/clust.PNG
docs/articles/coseq.PNG
docs/articles/dea.PNG
docs/articles/go.PNG
docs/articles/go_map.PNG
docs/articles/heatmap.PNG
docs/articles/import.PNG
docs/articles/index.html
docs/articles/maplot.PNG
docs/articles/mod.PNG
docs/articles/net.PNG
docs/articles/net_analysis.PNG
docs/articles/norm.PNG
docs/articles/pca.PNG
docs/articles/thr.PNG
docs/articles/venn.PNG
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/GENIE3OOB.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/abiotic_stresses.html
docs/reference/aggregate_splice_variants.html
docs/reference/app_ui.html
docs/reference/are_splice_variants.html
docs/reference/check_IDs.html
docs/reference/community_structure.html
docs/reference/convert_from_agi.html
docs/reference/convert_from_ensembl.html
docs/reference/convert_from_ensembl_ce.html
docs/reference/convert_from_ensembl_dm.html
docs/reference/convert_from_ensembl_eck12.html
docs/reference/convert_from_ensembl_mus.html
docs/reference/demo_data_At.html
docs/reference/describe_node.html
docs/reference/draw_DEGs-1.png
docs/reference/draw_DEGs.html
docs/reference/draw_MDS-1.png
docs/reference/draw_MDS.html
docs/reference/draw_PCA-1.png
docs/reference/draw_PCA.html
docs/reference/draw_coseq_run-1.png
docs/reference/draw_coseq_run-2.png
docs/reference/draw_coseq_run.html
docs/reference/draw_discarded_edges.html
docs/reference/draw_distributions-1.png
docs/reference/draw_distributions-2.png
docs/reference/draw_distributions.html
docs/reference/draw_enrich_go.html
docs/reference/draw_enrich_go_map-1.png
docs/reference/draw_enrich_go_map.html
docs/reference/draw_expression_levels-1.png
docs/reference/draw_expression_levels.html
docs/reference/draw_glm-1.png
docs/reference/draw_glm.html
docs/reference/draw_heatmap-1.png
docs/reference/draw_heatmap.html
docs/reference/draw_network.html
docs/reference/draw_network_degrees-1.png
docs/reference/draw_network_degrees.html
docs/reference/draw_profiles-1.png
docs/reference/draw_profiles-2.png
docs/reference/draw_profiles.html
docs/reference/draw_venn-1.png
docs/reference/draw_venn.html
docs/reference/enrich_go.html
docs/reference/enrich_go_custom.html
docs/reference/estimateDEGs.html
docs/reference/estimateDispersion.html
docs/reference/estimate_test_edges_time.html
docs/reference/figures/UI_teasing.PNG
docs/reference/figures/hex-DIANE.png
docs/reference/figures/net.PNG
docs/reference/figures/network.PNG
docs/reference/filter_low_counts.html
docs/reference/fit_glm.html
docs/reference/gene_annotations.html
docs/reference/get_correlation.html
docs/reference/get_factors_from_conditions.html
docs/reference/get_gene_information.html
docs/reference/get_genes_in_cluster.html
docs/reference/get_locus.html
docs/reference/get_nEdges.html
docs/reference/group_regressors.html
docs/reference/index.html
docs/reference/interGO.html
docs/reference/network_data.html
docs/reference/network_from_tests.html
docs/reference/network_inference.html
docs/reference/network_thresholding.html
docs/reference/normalize.html
docs/reference/plotDEGs-1.png
docs/reference/plotDEGs.html
docs/reference/regulators_per_organism.html
docs/reference/run_app.html
docs/reference/run_coseq.html
docs/reference/test_edges.html
inst/CITATION
inst/app/.DS_Store
inst/app/www/DIANE.png
inst/app/www/favicon.ico
inst/app/www/headerLogo.png
inst/app/www/hex-DIANE.png
inst/dependencies.R inst/extdata/DEA_report.Rmd inst/extdata/ICL.md inst/extdata/NEWS.md inst/extdata/clustering_report.Rmd inst/extdata/coseq.md inst/extdata/custom_go.md
inst/extdata/datasets/readme.rtf
inst/extdata/designFile.md inst/extdata/edgeR.md inst/extdata/ex_datasets.md inst/extdata/expressionFile.md
inst/extdata/favicon.ico
inst/extdata/filtering.md inst/extdata/genie3.md inst/extdata/inference_report.Rmd inst/extdata/infoFile.md inst/extdata/legal_mentions.md inst/extdata/logo_top.md inst/extdata/normalisation.md inst/extdata/normalisation_report.Rmd inst/extdata/pca.md inst/extdata/pglm.md inst/extdata/regulatorsFile.md inst/extdata/seed.md inst/extdata/tf_grouping.md inst/extdata/threshold.md inst/extdata/welcome.md
inst/golem-config.yml
logs/README.txt
man/GENIE3OOB.Rd man/abiotic_stresses.Rd man/aggregate_splice_variants.Rd man/app_ui.Rd man/are_splice_variants.Rd man/check_IDs.Rd man/community_structure.Rd man/convert_from_agi.Rd man/convert_from_ensembl.Rd man/convert_from_ensembl_ce.Rd man/convert_from_ensembl_dm.Rd man/convert_from_ensembl_eck12.Rd man/convert_from_ensembl_mus.Rd man/describe_node.Rd man/draw_DEGs.Rd man/draw_PCA.Rd man/draw_coseq_run.Rd man/draw_discarded_edges.Rd man/draw_distributions.Rd man/draw_enrich_go.Rd man/draw_enrich_go_map.Rd man/draw_expression_levels.Rd man/draw_glm.Rd man/draw_heatmap.Rd man/draw_network.Rd man/draw_network_degrees.Rd man/draw_profiles.Rd man/draw_venn.Rd man/enrich_go.Rd man/enrich_go_custom.Rd man/estimateDEGs.Rd man/estimateDispersion.Rd man/estimate_test_edges_time.Rd
man/figures/hex-DIANE.png
man/figures/net.PNG
man/filter_low_counts.Rd man/fit_glm.Rd man/gene_annotations.Rd man/get_correlation.Rd man/get_factors_from_conditions.Rd man/get_gene_information.Rd man/get_genes_in_cluster.Rd man/get_locus.Rd man/get_nEdges.Rd man/group_regressors.Rd man/interGO.Rd man/network_data.Rd man/network_from_tests.Rd man/network_inference.Rd man/network_thresholding.Rd man/normalize.Rd man/regulators_per_organism.Rd man/run_app.Rd man/run_coseq.Rd man/test_edges.Rd
shiny-customized.config
vignettes/.gitignore
vignettes/DIANE.Rmd vignettes/DIANE_Input_data.Rmd vignettes/DIANE_Programming_Interface.Rmd vignettes/DIANE_normalize.Rmd
vignettes/Heatmap.PNG
vignettes/clust.PNG
vignettes/coseq.PNG
vignettes/dea.PNG
vignettes/go.PNG
vignettes/go_map.PNG
vignettes/import.PNG
vignettes/maplot.PNG
vignettes/mod.PNG
vignettes/net.PNG
vignettes/net_analysis.PNG
vignettes/norm.PNG
vignettes/pca.PNG
vignettes/thr.PNG
vignettes/venn.PNG
OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.

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