Files in ctlab/phantasus
Visual and interactive gene expression analysis
.Rbuildignore
.dockerignore
.env
.gitignore
.gitmodules
.space.kts
.travis.yml
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
NEWS
R/adjustDataset.R
R/advancedNormalization.R
R/appConfig.R
R/calcPCA.R
R/calculatedAnnotation.R
R/collapseDataset.R
R/convertByAnnotationDB.R
R/createES.R
R/deseqAnalysis.R
R/es-data.R
R/fgseaTool.R
R/gseaPlot.R
R/limmaAnalysis.R
R/loadGEO.R
R/loadPreloaded.R
R/loadSession.R
R/performKmeans.R
R/phantasus-package.R
R/probeDataset.R
R/renameColumn.R
R/reproduceInR.R
R/serve.R
R/shinyGAM.R
R/subsetES.R
R/utils.R
README.md
appveyor.yml
data/es.rda
data/fgseaExample.rda
docker-compose.yml
inst/CITATION
inst/configs/R/phantasus/setup.yml
inst/configs/R/phantasus/user.conf
inst/configs/apache2/mods-available/mpm_prefork.conf
inst/configs/apache2/ports.conf
inst/configs/apache2/sites-available/000-default.conf
inst/configs/apache2/sites-available/opencpu.conf
inst/configs/index.html
inst/configs/nginx/nginx.conf
inst/configs/nginx/sites-available/default
inst/configs/opencpu/Rprofile
inst/configs/opencpu/server.conf
inst/docker-entrypoint.sh
inst/extdata/centers.gct
inst/gen_toy_mouse_matrix_h5.R
inst/test_js.sh
inst/testdata/GSE120978_unfiltered_pData.rda
inst/testdata/GSE27112-GPL6103.rda
inst/testdata/aa.rda
inst/testdata/annotationdb/sample_mouse_db.sqlite
inst/testdata/archs4/mouse_matrix.h5
inst/testdata/centers.gct
inst/testdata/collapse_dataset_one.gct
inst/testdata/config/R/phantasus/user.conf
inst/testdata/counts/archs4/human_matrix_v9_sample_100_100_1.h5
inst/testdata/counts/archs4/meta.txt
inst/testdata/counts/archs4/mouse_matrix_v9_sample_100_100_12.h5
inst/testdata/counts/counts_priority.txt
inst/testdata/counts/meta.rda
inst/testdata/counts_versioned_ids.gct
inst/testdata/dts.tsv
inst/testdata/geo/platforms/GPL17nnn/GPL17021/annot/GPL17021.soft
inst/testdata/geo/series/GSE99nnn/GSE99709/brief
inst/testdata/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz
inst/testdata/rows
inst/testdata/test.gct
inst/testdata/wrapped_aa.rda
inst/testdata/wrapped_wrongFormat.rda
inst/testdata/wrongFormatFile.rda
inst/update_js.sh
inst/update_static.sh
inst/update_versions.sh
inst/www/phantasus.js/.directory
inst/www/phantasus.js/RELEASE.js
inst/www/phantasus.js/bitmap.png
inst/www/phantasus.js/commit
inst/www/phantasus.js/css/images/icon.svg
inst/www/phantasus.js/css/images/phantasus_logo_16.png
inst/www/phantasus.js/css/images/phantasus_logo_main.svg
inst/www/phantasus.js/css/images/sort_asc.png
inst/www/phantasus.js/css/images/sort_asc_disabled.png
inst/www/phantasus.js/css/images/sort_both.png
inst/www/phantasus.js/css/images/sort_desc.png
inst/www/phantasus.js/css/images/sort_desc_disabled.png
inst/www/phantasus.js/css/images/ui-icons_444444_256x240.png
inst/www/phantasus.js/css/images/ui-icons_555555_256x240.png
inst/www/phantasus.js/css/images/ui-icons_777620_256x240.png
inst/www/phantasus.js/css/images/ui-icons_777777_256x240.png
inst/www/phantasus.js/css/images/ui-icons_cc0000_256x240.png
inst/www/phantasus.js/css/images/ui-icons_ffffff_256x240.png
inst/www/phantasus.js/css/phantasus-latest.min.css
inst/www/phantasus.js/css/phantasus.all.css
inst/www/phantasus.js/favicon.ico
inst/www/phantasus.js/fonts/FontAwesome.otf
inst/www/phantasus.js/fonts/fontawesome-webfont.eot
inst/www/phantasus.js/fonts/fontawesome-webfont.svg
inst/www/phantasus.js/fonts/fontawesome-webfont.ttf
inst/www/phantasus.js/fonts/fontawesome-webfont.woff
inst/www/phantasus.js/fonts/fontawesome-webfont.woff2
inst/www/phantasus.js/index.html
inst/www/phantasus.js/jasmine/SpecRunner.html
inst/www/phantasus.js/jasmine/lib/jasmine-2.5.2/boot.js
inst/www/phantasus.js/jasmine/lib/jasmine-2.5.2/console.js
inst/www/phantasus.js/jasmine/lib/jasmine-2.5.2/jasmine-html.js
inst/www/phantasus.js/jasmine/lib/jasmine-2.5.2/jasmine.css
inst/www/phantasus.js/jasmine/lib/jasmine-2.5.2/jasmine.js
inst/www/phantasus.js/jasmine/lib/jasmine-2.5.2/jasmine_favicon.png
inst/www/phantasus.js/jasmine/matchers/custom.js
inst/www/phantasus.js/jasmine/run_ocpu.js
inst/www/phantasus.js/jasmine/spec/adjust_tool_test.js
inst/www/phantasus.js/jasmine/spec/bivariate_functions_test.js
inst/www/phantasus.js/jasmine/spec/buffered_reader_test.js
inst/www/phantasus.js/jasmine/spec/collapse_tool_test.js
inst/www/phantasus.js/jasmine/spec/dataset_test.js
inst/www/phantasus.js/jasmine/spec/geo_reader_test.js
inst/www/phantasus.js/jasmine/spec/marker_selection_test.js
inst/www/phantasus.js/jasmine/spec/nearest_neighbors_test.js
inst/www/phantasus.js/jasmine/spec/preloaded_reader_test.js
inst/www/phantasus.js/jasmine/spec/qnorm_test.js
inst/www/phantasus.js/jasmine/spec/ranking_test.js
inst/www/phantasus.js/jasmine/spec/save_dataset_test.js
inst/www/phantasus.js/jasmine/spec/set_test.js
inst/www/phantasus.js/jasmine/spec/univariate_functions_test.js
inst/www/phantasus.js/jasmine/test_files/CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf.txt
inst/www/phantasus.js/jasmine/test_files/all_aml_train.gct
inst/www/phantasus.js/jasmine/test_files/aml_aml_train_marker_selection.gct
inst/www/phantasus.js/jasmine/test_files/aml_aml_train_nearest_neighbors_D50692_at.gct
inst/www/phantasus.js/jasmine/test_files/qnorm.gct
inst/www/phantasus.js/jasmine/test_files/simple_windows_test.txt
inst/www/phantasus.js/js/phantasus-external-other.min.js
inst/www/phantasus.js/js/phantasus-external-pdfkit-xlsx.min.js
inst/www/phantasus.js/js/phantasus-external-plotly-echarts.min.js
inst/www/phantasus.js/js/phantasus-external-plotly.min.js
inst/www/phantasus.js/js/phantasus.js
inst/www/phantasus.js/linking.html
inst/www/phantasus.js/message.proto
inst/www/phantasus.js/my.conf.js
inst/www/phantasus.js/package.json
inst/www/phantasus.js/phantasus-tutorial.html
inst/www/phantasus.js/server.js
inst/www/phantasus.js/sw.js
inst/www/phantasus.js/tutorial.html
man/adjustDataset.Rd
man/annotationDBMeta.Rd
man/calcPCA.Rd
man/calculatedAnnotation.Rd
man/checkGPLsFallback.Rd
man/checkGSEType.Rd
man/colMeansByGroups.Rd
man/collapseDataset.Rd
man/convertByAnnotationDB.Rd
man/createDockerConf.Rd
man/createES.Rd
man/es.Rd
man/fgseaExample.Rd
man/generatePreloadedSession.Rd
man/getArchs4Files.Rd
man/getCountsMetaPart.Rd
man/getES.Rd
man/getGDS.Rd
man/getGSE.Rd
man/getPhantasusConf.Rd
man/gseaPlot.Rd
man/isHSDS.Rd
man/limmaAnalysis.Rd
man/loadCounts.Rd
man/loadFromARCHS4.Rd
man/loadGEO.Rd
man/loadPreloaded.Rd
man/performKmeans.Rd
man/queryAnnotationDBMeta.Rd
man/read.gct.Rd
man/reparseCachedESs.Rd
man/reproduceInR.Rd
man/servePhantasus.Rd
man/setupPhantasus.Rd
man/shinyGAMAnalysis.Rd
man/subsetES.Rd
man/updateARCHS4.Rd
man/updateARCHS4meta.Rd
man/updateCountsMeta.Rd
man/updateDEE2meta.Rd
man/validateCountsCollection.Rd
man/write.gct.Rd
phantasus.Rproj
tests/testthat.R
tests/testthat/testAnnotationByDb.R
tests/testthat/testCollapse.R
tests/testthat/testcounts.R
tests/testthat/testcreateES.R
tests/testthat/testgseaPlot.R
tests/testthat/testkmeans.R
tests/testthat/testlimmaAnalysis.R
tests/testthat/testloadGEO.R
tests/testthat/testloadPreloaded.R
tests/testthat/testpcaPlot.R
tests/testthat/teststatic.R
vignettes/images/GSEA_plot.png
vignettes/images/adjust_tool.jpg
vignettes/images/annotation_result.png
vignettes/images/annotation_tool.png
vignettes/images/calculated_annotation_loaded.jpg
vignettes/images/calculated_annotation_tool.jpg
vignettes/images/collapse_tool.jpg
vignettes/images/dataset_loaded.jpg
vignettes/images/duplicates.jpg
vignettes/images/enrichr.png
vignettes/images/enrichr_result.png
vignettes/images/fgsea_genes.png
vignettes/images/fgsea_result.png
vignettes/images/fgsea_search.png
vignettes/images/fgsea_tool.png
vignettes/images/filter_tool.jpg
vignettes/images/filter_tool_result.jpg
vignettes/images/good_samples.jpg
vignettes/images/gse14308_norm.png
vignettes/images/hierarchical_tool.jpg
vignettes/images/huge_value.jpg
vignettes/images/kmeans_result.jpg
vignettes/images/kmeans_tool.jpg
vignettes/images/limma_results.png
vignettes/images/limma_tool.jpg
vignettes/images/link.png
vignettes/images/open_file_tool.jpg
vignettes/images/pcaplot_tool_clean.png
vignettes/images/pcaplot_tool_finished.png
vignettes/images/shiny_gam.jpg
vignettes/images/shiny_gam_result.jpg
vignettes/images/start_screen.jpg
vignettes/phantasus-tutorial.Rmd
