3ab211e351e6bce96fd5c2869a03fd00 *DESCRIPTION
e2d422e95fc799db685249e770d74dd2 *INSTALL.md
b759e53b8639e936b31ae559e7f2c166 *NAMESPACE
ae940d3213464457517791c8807dd485 *R/RFLOMICS-Class.R
775af025aa427dca0d27dd06489e92d4 *R/RFLOMICS-Generics.R
8c7156f78b0331e201510ca491dcc0bf *R/RFLOMICS-Methods_00_Common.R
d75ef7bfacb6d376e16c1204e6365128 *R/RFLOMICS-Methods_01_load_data.R
943b72755eb0da41d2117d7f04c6570f *R/RFLOMICS-Methods_02_set_stat_model.R
438db3ccf68f8076be8a032bfbdcfd85 *R/RFLOMICS-Methods_03_data_explor.R
a3743591200440ebbd563fdd37273f45 *R/RFLOMICS-Methods_04_diff_analysis.R
d7f8aa47e7d5b3bcf08ec8130388727f *R/RFLOMICS-Methods_05_coexp_analysis.R
8f2ccfbf7a109bc58dc73a3f9d01ea3a *R/RFLOMICS-Methods_06_annot_enrichment.R
f055cdb7d7a40eedd86d29d5579f4655 *R/RFLOMICS-Methods_07_Integration.R
97e2433bb98f205731a15dd768653554 *R/coverPage.R
11b52d37d90d31b386888b1ebf209dd8 *R/ecoseed.R
a67e45ed3651cc01d7a901ca71e17c2b *R/interface_docs.R
defeb021eb3b6da8ea3bbbfd69950ed5 *R/module_00_common.R
e25894f8dd22bdcaf4961016ba27e108 *R/module_01_load_data.R
e0dccfa9ee21436f5522b5eab416b538 *R/module_02_set_stat_model.R
b2c20c571bc034c7b08ba24a5332f73a *R/module_03_data_explor.R
b02bee876b6ad819370f93c082a4a5a8 *R/module_04_diff_analysis.R
af1f2b169f00c4b91ae67fac6b3dfef5 *R/module_05_coexp_analysis.R
85279e3ddeaf6237dc3b29d1e8a7e36d *R/module_06_annot_enrichment.R
07283bb467e686d2fa001e6818988355 *R/module_07_data_integration.R
647a8584a7ae08eb2faeabc4ac817694 *R/runRFLOMICS.R
36466d24f6aff49dfb6e2f1692aeee03 *R/server.R
3d49f275acce7f915e18817609c2c7db *R/ui.R
11b2c66e2fa95053837a3f432f9a336b *R/utils_00_common.R
967c39294942eec074bfd0d481b46946 *R/utils_01_load_data.R
9d787ec7d4a9780f1f14effc04883302 *R/utils_02_set_stat_model.R
3fe3a230d68a01e1f69dc64f46be1a56 *R/utils_03_data_explor.R
1f9e28070708ff69eee4b7487a86d521 *R/utils_04_diff_analysis.R
660ba44dd55dd8d2146fb2bb3ff53261 *R/utils_05_coexp_analysis.R
77064c11813c376452876cf63433402a *R/utils_06_annot_enrichment.R
527e595e7db54c0da2cc3e99c1114efd *R/utils_07_integration.R
d365f643b41576cddf80c0992dd76550 *README.md
20ed55ab8d8ff9a8a6eb4068cd7d26ca *build/vignette.rds
962591b4342423fb8dd469f88ed051cf *data/datalist
fa6606c88aaefa02b7427ca7602dd230 *data/ecoseed.df.rda
a733cf04f48cb9d889c8e79e3a17c611 *data/ecoseed.mae.rda
8eaf69baa2be4782a8cb3a22c9177062 *inst/NEWS.md
642263803a27401dcb5117724ade838b *inst/RFLOMICSapp/bibliography.bib
7992eccba08cbc81a467409a8156514a *inst/RFLOMICSapp/report.Rmd
3ee0f0986c9f6cfa2e09ff2598bd7ca2 *inst/RFLOMICSapp/report_01_omics.Rmd
87b902060a927ad5f9b884a237a45d9e *inst/RFLOMICSapp/report_02_design.Rmd
d1fc3b7d52b6d75f466e08868d6b77bf *inst/RFLOMICSapp/report_03_data_explor.Rmd
ab74dc5e5aed06e807631ea93b46b242 *inst/RFLOMICSapp/report_04_diff_analysis.Rmd
0c32dbc4cd8284c8313d36eba9d96122 *inst/RFLOMICSapp/report_04_diff_analysis_per_contrast.Rmd
679ed50e547e92f00ac7ebc6f2a5eac9 *inst/RFLOMICSapp/report_05_coexp_analysis.Rmd
83fa92c923c453799ce9d996681be3c8 *inst/RFLOMICSapp/report_06_enrichmentORA_analysis.Rmd
bb5d490aa664a98e4318310dfedc8a2e *inst/RFLOMICSapp/report_06_enrichmentORA_per_database.Rmd
297e7817f14ada9781cf399864c607ce *inst/RFLOMICSapp/report_06_enrichmentORA_per_list_CPR.Rmd
5a358a6be3beb6f4370ded09b11c7e38 *inst/RFLOMICSapp/report_07_MOFA2_integration.Rmd
f20f578883015d13441cbc3732dec9df *inst/RFLOMICSapp/report_08_mixOmics_integration.Rmd
836c03a3b41e031822cd2a3d47453013 *inst/RFLOMICSapp/www/IJPB_logo.png
bfbf2463ab28e5b52e393c08da3719a7 *inst/RFLOMICSapp/www/INRAE_logo.png
608a71011bd91c318f990061a1f24eed *inst/RFLOMICSapp/www/Install_clustermq.txt
1ca28510a953cb915a3136ce27780181 *inst/RFLOMICSapp/www/catiSysmics_logo.png
16e14de087d580cbb1073fd00bf2149a *inst/RFLOMICSapp/www/classesStyles.css
20fffa923c85b1a2ae439facd234827d *inst/RFLOMICSapp/www/style.css
ab300d90363396240ea2f1a37ac9c809 *inst/RFLOMICSapp/www/workflow.png
37fb17ea063a42cd62b1dc5b15079595 *inst/doc/RFLOMICS-command-line.R
3595e248fa4933af2bcae7f5957602ca *inst/doc/RFLOMICS-command-line.Rmd
d565a3b7d720b018f457088113553005 *inst/doc/RFLOMICS-command-line.html
c84e34ea656e25ba8f9556572ca0c016 *inst/doc/RFLOMICS-input-data.R
f3ec180848cfe2269cadac2a8e832381 *inst/doc/RFLOMICS-input-data.Rmd
f3a2ba301e6d95be539a89d52af6f8d3 *inst/doc/RFLOMICS-input-data.html
86bef48378f1c16bbe0a826475878afd *inst/doc/RFLOMICS.R
e01f002c2d0b0c197640378eb2c6db84 *inst/doc/RFLOMICS.Rmd
96de9e3b73fac9e1bc61eec35905bcec *inst/doc/RFLOMICS.html
809243e729da03395fe64d71bb2993fe *inst/examples/filterFeatures.R
1a3a26082e7b6ad911927f12c09eed17 *inst/examples/generateReport.R
a2fc85bea2672b001111a51668af13e5 *inst/examples/loadData.R
9e1d9c37e147d1f310240fe581a5c264 *inst/examples/prepareForIntegration.R
937e05b81a6640d605a27e856000b834 *inst/examples/runAnnotationEnrichment.R
e3c0a4be12f463b6e71ad689e90f8a14 *inst/examples/runCoExpression.R
6cecd197f87fb5cbacc035ef3ebba0a9 *inst/examples/runDataProcessing.R
0e73c12219aa85a1780f737d7d321266 *inst/examples/runDiffAnalysis.R
f06b866f06244a565d66befbe61be4da *inst/examples/runOmicsIntegration.R
7c59965dad519647f1a98b4efbb64f3c *inst/examples/statSetting.R
2c5e0821cada699b4714eb059999faf2 *man/RflomicsMAE-class.Rd
4d48bab662af4a7c178f3648621cffb7 *man/RflomicsSE-class.Rd
5dacfcaf7f41a4619a72cd453354929f *man/createRflomicsMAE.Rd
e3e705d5bcfc8e9a4a06c50446121620 *man/ecoseed.df.Rd
6a93f485224d195f27cd7aa67dafceec *man/ecoseed.mae.Rd
ab300d90363396240ea2f1a37ac9c809 *man/figures/workflow.png
15ca3aa86b95f8ce08348e63e25f5985 *man/generateExpressionContrast.Rd
7c1a5c5097b83a28ab9beeb9f3438a66 *man/generateModelFormulae.Rd
57eaaf2543bf83257f337f7efba8438b *man/generateReport.Rd
142d176803882725d2377866a2db61f9 *man/getAnalysis.Rd
87bf0b6a3f12c2b67787c1a4f62217e7 *man/prepareForIntegration.Rd
315228b4cbe3e39de0311c8da95f4f4b *man/rflomicsMAE2MAE.Rd
a98ea34985b247be23f25cdcb4a02d36 *man/runAnnotationEnrichment.Rd
ac768adaba2cc68675faa5d8083eaca0 *man/runCoExpression.Rd
85cb385cda247e9e2d5a27fdcbfd090d *man/runDataProcessing.Rd
20daaf8b032eae2a98c27f31cc66fc80 *man/runDiffAnalysis.Rd
e0959d750470c0eda8e9c6e79b762bb1 *man/runOmicsIntegration.Rd
b5c28ef6bb7a1f602622c54d12150ee0 *man/runRFLOMICS.Rd
0faba1fa9a883de27816765b68ce701f *tests/testthat.R
0a05b1f7941293611abedf100c9496ea *tests/testthat/test-0_reproducibility.R
780cac5999c1f69dea6b10e6a39376ca *tests/testthat/test-1_CreateRflomicsMAE.R
13a40f011e0249e583ed8a221ea8c770 *tests/testthat/test-2_setContrasts.R
a5ff8846002477eba5c75ddf638aa78e *tests/testthat/test-3_NormTransform.R
1a9b4e08d619c371a1d0606faa54e330 *tests/testthat/test-3_getProcessedData.R
8f7a2d0db09d80e55c48688e7142f984 *tests/testthat/test-3_runDataProcessing.R
78f3d7b3ac54e9f3a62303700b5b3601 *tests/testthat/test-4_DE.R
c7308283903c78237b03b4a997a867af *tests/testthat/test-5_coseq.R
8bf2bb9d3ff509fd612fbbd3232ca3a4 *tests/testthat/test-6_annotation.R
031a971e4f7cb103d36ed6eadeefcf9b *tests/testthat/test-7_MOFA.R
330ef1b09e4a36aae64dc63b7c2df92e *vignettes/Images/00_completeDesign.png
cc256f97302c357654b6d6148889499b *vignettes/Images/00_nonBalancedDesign.png
43379c598b1b4701c8afbad79bcc7544 *vignettes/Images/01_loadData.png
b0f3edb20b964d5202c14b41a0dec8e0 *vignettes/Images/02_setModel.png
86d7ec8e4c97a19f07174b9815eb2880 *vignettes/Images/03_DataProcess.png
386e46b1c71d133da48ccba7b7be05c5 *vignettes/Images/04_diffAnal.png
c81a0b8afa976dd2f8eae1917bda1d53 *vignettes/Images/05_coExpAnal.png
6f37149516d9faf91b2477256352bb71 *vignettes/Images/06_ORAAnal.png
1744e64807cb87af50100bee6e797b57 *vignettes/Images/07_MOFA.png
bf20d90e7cc28574aed3616a4c5ab366 *vignettes/Images/07_mixOmics.png
1326b954020fff9648e4242b5d481df5 *vignettes/Images/07_prepData.png
c659d5ea506d7881dfb01fec573a25d4 *vignettes/Images/DM_RflomicsMAE-design.png
592f62f64aa434145fa504faea217803 *vignettes/Images/DM_RflomicsMAE-integration.png
e8ad58457005743a24484b7b20c29035 *vignettes/Images/DM_RflomicsSE-overview.png
3595e248fa4933af2bcae7f5957602ca *vignettes/RFLOMICS-command-line.Rmd
f3ec180848cfe2269cadac2a8e832381 *vignettes/RFLOMICS-input-data.Rmd
e01f002c2d0b0c197640378eb2c6db84 *vignettes/RFLOMICS.Rmd
4346d615b44af3f487c289ff143a1823 *vignettes/bibliography.bib
