332b3092af4c64523b4fbc9bf85cd8c8 *DESCRIPTION
b09762b1876104452093414b59656a61 *LICENSE
e89f5f2700b5b4d07fbd135366b9c241 *NAMESPACE
0f98c01aae415a4e4925de496c8e093a *NEWS
db2100f9437ea21c1113ded6dac75329 *R/adjustDataset.R
a90e9d9ad8997efd1b64a2a65b325462 *R/advancedNormalization.R
e12b29b8ccc9f81b90be4a2127dae738 *R/appConfig.R
cb36933eaa86338839711e07a6a42936 *R/calcPCA.R
fa2d08121e7c5511707f922cc7e3986a *R/calculatedAnnotation.R
f86143709668571c9d7aa2380af785f0 *R/collapseDataset.R
4660a03054d39fa524b51fbbb86503e9 *R/convertByAnnotationDB.R
934dd81a3bc530196a20fed2c146628c *R/createES.R
7824452b3853636316013d16242f6fba *R/deseqAnalysis.R
d164cebb3c687311d5ca2297f165c984 *R/es-data.R
e1c8a76a354657ef5a804925d8e7166f *R/fgseaTool.R
e38b9912740bf47e51b55593a1a39491 *R/gseaPlot.R
c7baba6a23d07b5fee844d19e7402b76 *R/limmaAnalysis.R
7f773a119d30116472363bdeb0fc8a55 *R/loadGEO.R
803c9c9ff9cf4752d62a2bb1eb79677d *R/loadPreloaded.R
4b270d45b8736e57f8b22d3af92acc7b *R/loadSession.R
9f1941bb6652cf8aae12097c4ccfcc0f *R/performKmeans.R
d34df66ccb346f2fcd92d4638460bd50 *R/phantasus-package.R
7204c25877fa74830fee69795c7ca942 *R/probeDataset.R
e6e2067d43a7862fd103f121648e099f *R/renameColumn.R
c2fe22db347e3545875da3394d813d8a *R/reproduceInR.R
36b96f7376a7e7dca29feff78178d312 *R/serve.R
3dbac31c002cc0c103fc602928f4c436 *R/shinyGAM.R
754d00302a5c3137aea7262b6283c08c *R/subsetES.R
0c28d032a2078d24c84e74c05b6cc4d3 *R/utils.R
fe9bbd45c253a53632c12893d9e7570b *README.md
8a18b60355bd94349a995238674d197f *data/es.rda
a796a489cacab3b0a1d3af2a0d04105f *data/fgseaExample.rda
80c74d50ff056a74cc9475d5a0b3d7a1 *inst/CITATION
e025fc9dd20a633fa9cd395618b3a712 *inst/configs/R/phantasus/setup.yml
f22e47cfc3a23c4a6eab33f4bef9dd4b *inst/configs/R/phantasus/user.conf
9f2e1fe1682763f54fced36131e5f67a *inst/configs/apache2/mods-available/mpm_prefork.conf
479c079d6ff4b3354bd5c48bd3fb75c2 *inst/configs/apache2/ports.conf
16813665c14bd96f0f1b6b1c57828433 *inst/configs/apache2/sites-available/000-default.conf
1bfbefb7bb1e349a098c372928776898 *inst/configs/apache2/sites-available/opencpu.conf
b50fb1203761197ff7b2afddec8e35a8 *inst/configs/index.html
763ec90db83aa5e2ddca4daf0fd063a8 *inst/configs/nginx/nginx.conf
16207b683c5ee197c0ab672b12bceecb *inst/configs/nginx/sites-available/default
3a1c7e26bea2a1538adea5b7a8fbce30 *inst/configs/opencpu/Rprofile
e3d4c12bf9dc3d9a2857d0c97e050cb7 *inst/configs/opencpu/server.conf
18bea1651c0071070115ff3779eb4d3e *inst/doc/phantasus-tutorial.R
181224b0dc318f5845cf07f4a6d04451 *inst/doc/phantasus-tutorial.Rmd
6fcf6098b0cb983cef74dd53dc7da53d *inst/doc/phantasus-tutorial.html
20821c516cc498aa67b243aa8ed3ae40 *inst/docker-entrypoint.sh
ac734b243283b53f07939630b596580a *inst/extdata/centers.gct
28a6da62ad244eb124b44dea6840579d *inst/gen_toy_mouse_matrix_h5.R
11c71644b7168d173071dc6141bbd2d3 *inst/testdata/GSE120978_unfiltered_pData.rda
8864a1561444a60672ecbc1037042ad0 *inst/testdata/GSE27112-GPL6103.rda
5df28083c7a252044aa9872a87a2f090 *inst/testdata/aa.rda
4fb911ac7cce878b07ab25f1740c721a *inst/testdata/annotationdb/sample_mouse_db.sqlite
5254de904e1488bbfa8fa5d87adf11fc *inst/testdata/archs4/mouse_matrix.h5
00b188790f2c7f345ee0e84330d3e118 *inst/testdata/centers.gct
24b99d862c112f6810a64d6276eac427 *inst/testdata/collapse_dataset_one.gct
de068271e22e3c16ebddf7ee482391ed *inst/testdata/config/R/phantasus/user.conf
7e505881acc3022bf9e8ad8d23e983c2 *inst/testdata/counts/archs4/human_matrix_v9_sample_100_100_1.h5
bea4cb156fa306001f60917d9a6ef403 *inst/testdata/counts/archs4/meta.txt
681cfc65cf6c242e4f94a3c95df729a9 *inst/testdata/counts/archs4/mouse_matrix_v9_sample_100_100_12.h5
20032740052dcfc1db81bfcecb5c4870 *inst/testdata/counts/counts_priority.txt
f0da05737f625a02a11c78606d01b802 *inst/testdata/counts/meta.rda
f482701450f3db4eacdb63a1be56765b *inst/testdata/counts_versioned_ids.gct
899f5a79d5583f942f03b425249357b2 *inst/testdata/dts.tsv
92fa4e12f19d8515ed24a8dd716d2a88 *inst/testdata/geo/platforms/GPL17nnn/GPL17021/annot/GPL17021.soft
9133ec3fcfd6d70812c958cfc3bbe682 *inst/testdata/geo/series/GSE99nnn/GSE99709/brief
eae4f3a601613fc52fc73819bf682a1a *inst/testdata/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz
a77f54ce8abe2e2377e923ffd69426a2 *inst/testdata/rows
455a71a71f8f97a3f8e089d271d5a486 *inst/testdata/test.gct
4557c2d25ec7f884dd0111ad4fe065dc *inst/testdata/wrapped_aa.rda
80a7b5302414e9a5758ea489d4d322df *inst/testdata/wrapped_wrongFormat.rda
6a9020de26af1075c4d1e4e5eccbabf8 *inst/testdata/wrongFormatFile.rda
97b22b41782a1d25f998fdae964ae42b *inst/update_js.sh
4022e1f5919c16635253661e752b6914 *inst/update_versions.sh
cccdbb272d2de1c6b60ff90a35a8bbe9 *inst/www/phantasus.js/RELEASE.js
72ae361ac856eabdd24501882169e8a3 *inst/www/phantasus.js/bitmap.png
19238bd4bc57717f0403cba8b029a68e *inst/www/phantasus.js/commit
d044d90cd66e10c9f90f17daa923336c *inst/www/phantasus.js/css/images/icon.svg
63c4fb6f7de5c4c85156661a73c3c287 *inst/www/phantasus.js/css/images/phantasus_logo_16.png
5323d786155a91a12bb8667346a4b391 *inst/www/phantasus.js/css/images/phantasus_logo_main.svg
9326ad44ae4bebdedd141e7a53c2a730 *inst/www/phantasus.js/css/images/sort_asc.png
d7dc10c78f23615d328581aebcd805eb *inst/www/phantasus.js/css/images/sort_asc_disabled.png
9a6486086d09bb38cf66a57cc559ade3 *inst/www/phantasus.js/css/images/sort_both.png
1fc418e33fd5a687290258b23fac4e98 *inst/www/phantasus.js/css/images/sort_desc.png
bda51e15154a18257b4f955a222fd66f *inst/www/phantasus.js/css/images/sort_desc_disabled.png
f4ebe485bc50abaf580cf6ae9895dde5 *inst/www/phantasus.js/css/images/ui-icons_444444_256x240.png
d70c49a1750e399344e77737be6eac71 *inst/www/phantasus.js/css/images/ui-icons_555555_256x240.png
03c85664fb3ba7db61e1b0c6da73b1ae *inst/www/phantasus.js/css/images/ui-icons_777620_256x240.png
6d28e77dd32aa1e61433d5ba3d93ca86 *inst/www/phantasus.js/css/images/ui-icons_777777_256x240.png
bd6996f9c0921f5e744aba81d3dadd84 *inst/www/phantasus.js/css/images/ui-icons_cc0000_256x240.png
e33c878c8e1b176d439484ca0a094ec4 *inst/www/phantasus.js/css/images/ui-icons_ffffff_256x240.png
1bb38f74d430c9f7a57e4969f32fddb1 *inst/www/phantasus.js/css/phantasus-latest.min.css
1c0a9ac8df35c1a4815f077866a62040 *inst/www/phantasus.js/favicon.ico
5dc41d8fe329a22fa1ee9225571c843e *inst/www/phantasus.js/fonts/FontAwesome.otf
25a32416abee198dd821b0b17a198a8f *inst/www/phantasus.js/fonts/fontawesome-webfont.eot
d7c639084f684d66a1bc66855d193ed8 *inst/www/phantasus.js/fonts/fontawesome-webfont.svg
1dc35d25e61d819a9c357074014867ab *inst/www/phantasus.js/fonts/fontawesome-webfont.ttf
c8ddf1e5e5bf3682bc7bebf30f394148 *inst/www/phantasus.js/fonts/fontawesome-webfont.woff
e6cf7c6ec7c2d6f670ae9d762604cb0b *inst/www/phantasus.js/fonts/fontawesome-webfont.woff2
a6a8ef3fdf4cde4f0ca4258448d00c5b *inst/www/phantasus.js/index.html
de6b567d3ea2e40504dd02928a3e8ece *inst/www/phantasus.js/js/phantasus-external-other.min.js
bf495f35623c90ef725e0bc173138031 *inst/www/phantasus.js/js/phantasus-external-pdfkit-xlsx.min.js
caa5cf769f07009c2e18204a511a1081 *inst/www/phantasus.js/js/phantasus-external-plotly-echarts.min.js
0ecb7e9206937cc601d37c5f9095f444 *inst/www/phantasus.js/js/phantasus-external-plotly.min.js
6be9345f69d73ee2e22304405e00be7c *inst/www/phantasus.js/js/phantasus.js
be7b2951e9424873569330ed83f75f6d *inst/www/phantasus.js/linking.html
c09f073a5453611bef272bd6a65112c1 *inst/www/phantasus.js/message.proto
9fc7617ba54d479bb191526096e75fd2 *inst/www/phantasus.js/phantasus-tutorial.html
719ce00894fa1b9891698215de821dc0 *inst/www/phantasus.js/server.js
9fe32651de05747d9c31f2f7de86c39f *inst/www/phantasus.js/sw.js
4a77c90d1109272965e6bc907101d264 *inst/www/phantasus.js/tutorial.html
ac333f80e3dcd0b071267254512030b6 *man/adjustDataset.Rd
91b1b2d35e383cd073836fb01421bfa6 *man/annotationDBMeta.Rd
7d5e081b87ff296b6f767a91154b1c13 *man/calcPCA.Rd
50dcc99e7c0843ac5580ab5b6304fef7 *man/calculatedAnnotation.Rd
fad1c930dc94df77a64dc8ff46e68540 *man/checkGPLsFallback.Rd
4f87d848a4281b9790014bcacf1f2735 *man/checkGSEType.Rd
27adac3b93836cdd076a8a2836c3f00b *man/colMeansByGroups.Rd
20e84809a9b069ffa30eb5071ae8a166 *man/collapseDataset.Rd
5da8ee9fc9bf78e0c4cd492f91ed7932 *man/convertByAnnotationDB.Rd
deb13d860439ec2a4b8f3c9f0b7c99c3 *man/createDockerConf.Rd
d30447c6ad2b1d6eb47425fe6e6a73f5 *man/createES.Rd
25460e08878f25a6d8898c9889ed5174 *man/es.Rd
e52471a03f07a4e2f1eb98ed7de578e2 *man/fgseaExample.Rd
b1596d317dc4df39fca202fa12e25110 *man/generatePreloadedSession.Rd
7664c3b77a5e6cb994a9c5dfe3d507ba *man/getArchs4Files.Rd
3d635af4ae31e7ad887516fb7c313d41 *man/getCountsMetaPart.Rd
bc7985fef57c5df7a638f1603fb570f9 *man/getES.Rd
beba35fc06bbd9c25491c3cbfc170436 *man/getGDS.Rd
eea2954f3f1a3f5acae5d571293bbc21 *man/getGSE.Rd
ffa35cc9b8b38e44fc233f9570b0dcf1 *man/getPhantasusConf.Rd
69cdee524c2ddd103ccb25f08e907666 *man/gseaPlot.Rd
c7476851c9f6a156d4143403bdc9632b *man/isHSDS.Rd
d4c625de8821ccf99bb86f3267d762b2 *man/limmaAnalysis.Rd
cab902e971b36eed7ae18cb9dc94458a *man/loadCounts.Rd
5ff7df34673195a2cfa0dd3b637738be *man/loadFromARCHS4.Rd
8d060995dc5ca93500416660eaab4c7c *man/loadGEO.Rd
660d9e28deee4eb3073e327e69a3919a *man/loadPreloaded.Rd
e0b65a1679249d1d9b56f68dd071c840 *man/performKmeans.Rd
261dbde320d61fd46dee226694b6728a *man/queryAnnotationDBMeta.Rd
8848918c3b8c38a31668fd4991df2879 *man/read.gct.Rd
225230ed95eb9ad6b098ed590f377dca *man/reparseCachedESs.Rd
9196ddb0077a26f5c6b0d5d8ab5e3c97 *man/reproduceInR.Rd
00b50ca0e513b821827d6bebee75ef2b *man/servePhantasus.Rd
3384706d84c7e3785bda4130304a8052 *man/setupPhantasus.Rd
f396bf1733898dca1c3d76c2e21d0d93 *man/shinyGAMAnalysis.Rd
bd2e2c262abf7e74b03eb9604359c30f *man/subsetES.Rd
d7c07ec41d2f52232572f5f08fc5c59d *man/updateARCHS4.Rd
25d9563d11bb0323bc5b2fb0f4bcf621 *man/updateARCHS4meta.Rd
78178fb4c3771424e04ea01287ec8280 *man/updateCountsMeta.Rd
177e0b057c63e2ed0710e9f2eb347cdd *man/updateDEE2meta.Rd
3387567c2a690dd95086950fe150dd6f *man/validateCountsCollection.Rd
8b622979b8d03ae33fe13a6182d27282 *man/write.gct.Rd
3a879dee1a714ba194951abafd612fde *tests/testthat.R
404597828e8a7d233b7ed8894c12e640 *tests/testthat/testAnnotationByDb.R
a8d9e019a3c56a5836fcf057c653d355 *tests/testthat/testCollapse.R
8c44de6cfe6b9be784e9af4194303c1a *tests/testthat/testcounts.R
03763df50dc7ab21bd7fed1255651b2f *tests/testthat/testcreateES.R
937aac129f5a66ca7078d73680cb5e9e *tests/testthat/testgseaPlot.R
c08ef408cd6bad72391522784cbc3f48 *tests/testthat/testkmeans.R
d7aa2e1575706eb98e06576387ca182d *tests/testthat/testlimmaAnalysis.R
c95d657beeb60ca80dd4400b1df0d371 *tests/testthat/testloadGEO.R
47002f60f9a892612989344bde2e8fcb *tests/testthat/testloadPreloaded.R
775a39b8df13a29f951e341de18e05c5 *tests/testthat/testpcaPlot.R
2d65c8ed08469771e56eeb8a1a509bee *tests/testthat/teststatic.R
864f635f21300d173aa6de36bf4304cc *vignettes/images/GSEA_plot.png
4345381bcea9797e7fe6a3bcbaefe14a *vignettes/images/adjust_tool.jpg
9bc4ab19ad440980e847b12af7669140 *vignettes/images/annotation_result.png
b60265955ac2183699887a036f7c0509 *vignettes/images/annotation_tool.png
aebbcb4f76a33de38ef42c7e057d9166 *vignettes/images/calculated_annotation_loaded.jpg
112a2142616221dce5c759cc684d0ef9 *vignettes/images/calculated_annotation_tool.jpg
ce127db0ec48afecda837709beb925fb *vignettes/images/collapse_tool.jpg
1c9ef0a6f2fa770163ccd37af6f7f266 *vignettes/images/dataset_loaded.jpg
18ac86ef387632b9468773de6c2c7a40 *vignettes/images/duplicates.jpg
8bc8eabdefcf66b841760307a32fa0b9 *vignettes/images/enrichr.png
d159afa1c611adedb85e57397050c364 *vignettes/images/enrichr_result.png
0b23ac48cf899718d23e4c9ec5d1e3b3 *vignettes/images/fgsea_genes.png
81fe1b936403602a8fc4718ed01f15b7 *vignettes/images/fgsea_result.png
7aba8a0cabc02e84ad4e48a12b3db043 *vignettes/images/fgsea_search.png
ad981aab202e63a183e8948c0f0d2826 *vignettes/images/fgsea_tool.png
f735c7010980af6673b34d5082504d74 *vignettes/images/filter_tool.jpg
d55760b6635b161caf302659d747c6d5 *vignettes/images/filter_tool_result.jpg
3bf4182cb86e41160de5f89e5da8e1c4 *vignettes/images/good_samples.jpg
82e64b0f51a2b6f9e9d364cd70602662 *vignettes/images/gse14308_norm.png
c3e1ee64a632d25064cec50d1d4f7510 *vignettes/images/hierarchical_tool.jpg
ed54233438ff8974d23b841f9f528e61 *vignettes/images/huge_value.jpg
fc2f5f92ec5784b7dbde2e78890a234f *vignettes/images/kmeans_result.jpg
e972c1854fb360dc23f733388a50dcee *vignettes/images/kmeans_tool.jpg
e29c315781df71a3eef43aba48559b8b *vignettes/images/limma_results.png
5868a4d66121ca1cf9772f5c6aa7f1b3 *vignettes/images/limma_tool.jpg
9e3d266a7ee844b9b190a4abed9289f7 *vignettes/images/link.png
ca3d301765261d63f7f144f1054adc3d *vignettes/images/open_file_tool.jpg
07e02a1309361343b41aebfc6a6846cc *vignettes/images/pcaplot_tool_clean.png
8e921c24f61ef571e7dba6423dc3607d *vignettes/images/pcaplot_tool_finished.png
bb0178ac70906bd7f814585acaa3a789 *vignettes/images/shiny_gam.jpg
644fbf1da8e6e7b7ec29c9ac6874d605 *vignettes/images/shiny_gam_result.jpg
8765dffbe7b7d92167f773e592001c1a *vignettes/images/start_screen.jpg
181224b0dc318f5845cf07f4a6d04451 *vignettes/phantasus-tutorial.Rmd
