Files in phantasus

Visual and interactive gene expression analysis

README.md

NEWS

NAMESPACE

DESCRIPTION

LICENSE

data/fgseaExample.rda

data/es.rda

R/es-data.R R/probeDataset.R R/adjustDataset.R R/subsetES.R R/performKmeans.R R/fgseaTool.R R/limmaAnalysis.R R/reproduceInR.R R/loadSession.R R/calculatedAnnotation.R R/shinyGAM.R R/serve.R R/loadPreloaded.R R/loadGEO.R R/utils.R R/renameColumn.R R/calcPCA.R R/createES.R R/phantasus-package.R R/gseaPlot.R R/deseqAnalysis.R R/collapseDataset.R R/convertByAnnotationDB.R vignettes/phantasus-tutorial.Rmd

vignettes/images/filter_tool_result.jpg

vignettes/images/enrichr_result.png

vignettes/images/dataset_loaded.jpg

vignettes/images/limma_tool.jpg

vignettes/images/annotation_tool.png

vignettes/images/fgsea_search.png

vignettes/images/GSEA_plot.png

vignettes/images/calculated_annotation_loaded.jpg

vignettes/images/hierarchical_tool.jpg

vignettes/images/collapse_tool.jpg

vignettes/images/shiny_gam_result.jpg

vignettes/images/huge_value.jpg

vignettes/images/kmeans_tool.jpg

vignettes/images/fgsea_genes.png

vignettes/images/shiny_gam.jpg

vignettes/images/fgsea_result.png

vignettes/images/limma_results.png

vignettes/images/adjust_tool.jpg

vignettes/images/fgsea_tool.png

vignettes/images/pcaplot_tool_finished.png

vignettes/images/duplicates.jpg

vignettes/images/annotation_result.png

vignettes/images/kmeans_result.jpg

vignettes/images/filter_tool.jpg

vignettes/images/pcaplot_tool_clean.png

vignettes/images/link.png

vignettes/images/good_samples.jpg

vignettes/images/enrichr.png

vignettes/images/calculated_annotation_tool.jpg

vignettes/images/open_file_tool.jpg

vignettes/images/start_screen.jpg

vignettes/images/gse14308_norm.png

man/calculatedAnnotation.Rd man/servePhantasus.Rd man/shinyGAMAnalysis.Rd man/adjustDataset.Rd man/loadPreloaded.Rd man/getArchs4Files.Rd man/generatePreloadedSession.Rd man/limmaAnalysis.Rd man/checkGPLsFallback.Rd man/read.gct.Rd man/reproduceInR.Rd man/getES.Rd man/colMeansByGroups.Rd man/loadFromARCHS4.Rd man/convertByAnnotationDB.Rd man/fgseaExample.Rd man/collapseDataset.Rd man/performKmeans.Rd man/calcPCA.Rd man/subsetES.Rd man/queryAnnotationDBMeta.Rd man/es.Rd man/reparseCachedESs.Rd man/loadGEO.Rd man/getGSE.Rd man/annotationDBMeta.Rd man/getGDS.Rd man/gseaPlot.Rd man/write.gct.Rd man/createES.Rd tests/testthat.R tests/testthat/testgct.R tests/testthat/testgseaPlot.R tests/testthat/testloadGEO.R tests/testthat/testlimmaAnalysis.R tests/testthat/testkmeans.R tests/testthat/testloadPreloaded.R tests/testthat/testcreateES.R tests/testthat/testpcaPlot.R tests/testthat/testCollapse.R

inst/update_js.sh

inst/gen_toy_mouse_matrix_h5.R

inst/CITATION

inst/docker-entrypoint.sh

inst/doc/phantasus-tutorial.html

inst/doc/phantasus-tutorial.Rmd inst/doc/phantasus-tutorial.R

inst/configs/index.html

inst/configs/apache2/ports.conf

inst/configs/apache2/sites-available/opencpu.conf

inst/configs/apache2/sites-available/000-default.conf

inst/configs/apache2/mods-available/mpm_prefork.conf

inst/configs/nginx/nginx.conf

inst/configs/nginx/sites-available/default

inst/configs/opencpu/Rprofile

inst/configs/opencpu/server.conf

inst/www/phantasus.js/index.html

inst/www/phantasus.js/server.js

inst/www/phantasus.js/message.proto

inst/www/phantasus.js/linking.html

inst/www/phantasus.js/RELEASE.js

inst/www/phantasus.js/favicon.ico

inst/www/phantasus.js/commit

inst/www/phantasus.js/sw.js

inst/www/phantasus.js/phantasus-tutorial.html

inst/www/phantasus.js/tutorial.html

inst/www/phantasus.js/js/phantasus-external-plotly.min.js

inst/www/phantasus.js/js/phantasus-external-pdfkit-xlsx.min.js

inst/www/phantasus.js/js/phantasus-external-other.min.js

inst/www/phantasus.js/js/phantasus.js

inst/www/phantasus.js/js/phantasus-external-plotly-echarts.min.js

inst/www/phantasus.js/fonts/fontawesome-webfont.svg

inst/www/phantasus.js/fonts/FontAwesome.otf

inst/www/phantasus.js/fonts/fontawesome-webfont.woff2

inst/www/phantasus.js/fonts/fontawesome-webfont.woff

inst/www/phantasus.js/fonts/fontawesome-webfont.eot

inst/www/phantasus.js/fonts/fontawesome-webfont.ttf

inst/www/phantasus.js/css/phantasus-latest.min.css

inst/www/phantasus.js/css/images/ui-icons_ffffff_256x240.png

inst/www/phantasus.js/css/images/sort_asc.png

inst/www/phantasus.js/css/images/sort_desc_disabled.png

inst/www/phantasus.js/css/images/ui-icons_777620_256x240.png

inst/www/phantasus.js/css/images/sort_desc.png

inst/www/phantasus.js/css/images/ui-icons_444444_256x240.png

inst/www/phantasus.js/css/images/ui-icons_cc0000_256x240.png

inst/www/phantasus.js/css/images/icon.svg

inst/www/phantasus.js/css/images/sort_both.png

inst/www/phantasus.js/css/images/sort_asc_disabled.png

inst/www/phantasus.js/css/images/ui-icons_777777_256x240.png

inst/www/phantasus.js/css/images/ui-icons_555555_256x240.png

inst/extdata/centers.gct

inst/testdata/wrapped_wrongFormat.rda

inst/testdata/collapse_dataset_one.gct

inst/testdata/GSE27112-GPL6103.rda

inst/testdata/test.gct

inst/testdata/wrongFormatFile.rda

inst/testdata/centers.gct

inst/testdata/rows

inst/testdata/wrapped_aa.rda

inst/testdata/aa.rda

inst/testdata/dts.tsv

inst/testdata/archs4/mouse_matrix.h5

inst/testdata/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz

inst/testdata/geo/platforms/GPL17nnn/GPL17021/annot/GPL17021.soft

phantasus documentation built on Nov. 8, 2020, 6:39 p.m.