56e2c5f772c8bbb9683ef1a2b04d6ad0 *DESCRIPTION
5eadd12688c7271602f88620680f3793 *NAMESPACE
87d067ffbba790f6b10802b4b4cc80f1 *NEWS
9e75de4fdcba04d22d389476a8ac2d1b *R/AUCell.R
dada8e249194cc20a10a959ccb58c98e *R/AUCell_multiple_genesets.R
694a59e600b11d90854f3cdef6d90605 *R/Bulk_EMTscore.R
7ee3024227426e88d23f0e009c14454f *R/Calculate_Signature_score.R
7d0c31fc16f193de9d4265e3fc60b970 *R/EMTscore-package.R
8f652f9665292b4f4bb75da6f6e31783 *R/EMTscore_plot.R
23bf6bf467e22230c3c7142520b6cc26 *R/EM_state_classification.R
4ffdd8f6afc2a9d1c3e5780b72c8f168 *R/GSVA.R
df118ef6203d74421f060d792be6a5db *R/GSVA_multiple_genesets.R
75d5c2b30ab79b61bc0e52400ecd44d8 *R/JASMINE.R
ac2eb246ab255e7dff7a0bf350c2eead *R/JASMINE_multiple_genesets.R
bec6d03c25b5a21f363f20179928b796 *R/Pathway_score_correlation.R
266eff9a12a1b2588badc08d7aeb7173 *R/SCSE.R
7a22dd71371cfd8a67d8849328e58e38 *R/SCSE_multiple_genesets.R
0b01b0d9e30e73089141897433880970 *R/Singlecell_EMTscore.R
81afbcf6045b95fa96e60294aea65c02 *R/data.R
33f098c61f1b4f2634e8bf8ab9bee0dd *R/generate_gmt_from_genelists.R
6d1d0679ae142fb55edbf21f5e37e70f *R/nnPCA.R
361b8d370dd7b73a3d93e9fa58b0622e *R/nnPCA_multiple_genesets.R
1aa3588dee919fd15eabdf73c0a4c932 *R/parallel_helper.R
bfab34f9a9c1a049a45ccadfd02f7890 *R/ssGSEA.R
786493a69e5c191f982a8ffe5acc8d9c *R/ssGSEA_multiple_genesets.R
fa6e310f9b7fc43967f22d227e3305f3 *R/utils.R
f3b8faa4259b2f6f51eacb45e0952dd9 *README.md
21c9401b8c07f38d762ade4612fc4ffe *build/partial.rdb
f5854028a742a2194a39e05b891a3f4a *build/vignette.rds
19df6663c7bea177449e994379d598ac *data/GO.rda
c420bfcd566d735b5b2161a52b8cb2aa *data/MSigDB_Hallmark.rda
313645c2434fabd707df4dfaa7f40c6e *data/Panchy_et_al_E_signature.rda
226473aa1b4486334c622a3e2994c703 *data/Panchy_et_al_M_signature.rda
ecdc68073c3b21e69bae90d877a67147 *data/SCSE_Result_EMT.rda
7c6ba8313c186d329a2cd17b95f7d7c5 *data/Tan_et_al_cell_line_E_signature.rda
cefc47142970a619dbed63065538af3a *data/Tan_et_al_cell_line_M_signature.rda
67d3eaaf143b924d8ef0b922f69cb616 *data/Tan_et_al_tumor_E_signature.rda
7a30c023a74eb42e5c1b1b61972f0754 *data/Tan_et_al_tumor_M_signature.rda
3887f90aa1507e56a9eac4bf47539678 *data/cell_annotation_file.rda
c03e9eaa2b99421b58e09d53cbfa8221 *data/data_for_plot.rda
1b730e0956807c7945e728079a4efbae *data/geneExp.rda
80b51c7d5e4a020158694e60c35c90b7 *data/nnPCA_Result_EMT.rda
35e657f8e39a1d36044541766b392be7 *data/nnPCA_Result_multiple.rda
6bb168d4691c390b688adbd3e3e30b9c *inst/CITATION
18caeafcc71d5a9573dcb242dfa750cb *inst/doc/EMTscore.R
c73bb78d85df03c0b06d7ad2bcb7c01c *inst/doc/EMTscore.Rmd
c93d5be20430765f43e1c26d10f7ebbc *inst/doc/EMTscore.html
0d6a702ba8be0df17eb391c063903cd2 *inst/extdata/Christian2012
ff0b4b980573b03d06a4092c0306bf50 *inst/extdata/EMTome_signatures.gmt
eb86cb4933b7f40b809cb9d5a1acbd42 *inst/extdata/EM_signature.gmt
e4dbcce2aab743dfb967528be0d205f6 *inst/extdata/E_signature.gmt
acc96077aaac0a9e58ff87aed719a2eb *inst/extdata/HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.v2025.1.Hs.gmt
518ce5729130a4f241d0f93255c36a67 *inst/extdata/Joseph2010
b0ca40586d9c32daa3c4527cbea930f2 *inst/extdata/Joseph2015
7854602584f295083a49d695354cbcd3 *inst/extdata/Khalil2024_E
9ac89d7c77ec35596029b5934d94fd0b *inst/extdata/Khalil2024_M
e75871f70f01a0cb3ea207c7001b00c4 *inst/extdata/Liutao_2016
cfed866751c9384ce04a0ce226453f0c *inst/extdata/M_signature.gmt
026006ef6d6a7a074e4691f034a88616 *inst/extdata/Momeneh2017
94e5e927d1c16fdca69fec3ff09e83c0 *inst/extdata/TianLab_collected_EMT_signatures.gmt
0397dd8b6442d0535bad60c1eaa1aeb2 *inst/extdata/cellular_senescence_sig.tsv
c0120b257ee55abc00db099a115b5ce7 *inst/extdata/combined2_EM_signature.gmt
da109301d6417ccedf195e20dd6a9f55 *inst/extdata/combined_EM_signature.gmt
74571b2d7c8e5006327f5fb05342a869 *inst/extdata/david_p_cook
135579969c4ed89a31eecaddb7c29d19 *inst/extdata/example_sce.rds
4912cbccb3235f8555eaf9172e2bf312 *inst/extdata/example_seurat_obj.rds
51d25f9b6d34bc98bf583b3cf6bfbb6f *inst/extdata/filtered.c2.gmt
ccb79604c80d66bc5990b27f1c68d23d *inst/extdata/h.all.v2025.1.Hs.symbols.gmt
0ba79a3c7cf231fca05889b78dde2d7a *inst/extdata/merged_genes.rda
82511593874889267e5590450dba2800 *inst/extdata/mouse_EM_signature.gmt
145023794c5e8fa588e11d1e2d843058 *inst/extdata/mouse_emt.gmt
5ba7ab352685dfa0844817f269999105 *inst/extdata/simulated.R
3fc08f07a898c53180f4205ece8fd67a *inst/extdata/stemsig.tsv
acc96077aaac0a9e58ff87aed719a2eb *inst/extdata/test.gmt
88298b967366ad03ca1ecf167b1a09ae *inst/script/make-data.R
2f4ec04a619229c5025d6a675f5a70d0 *inst/script/make_geneExp.R
ff4e52b456b84461113d8146b6f8fd0d *man/Arrange_plots.Rd
d544c458e5b21511e426429c81527fae *man/EMTscore-package.Rd
3c0fc009172cdb977f02e3b5f4dd4933 *man/Execute_AUCell.Rd
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19fb88b3af5029fe8d518c38aa5e95d9 *man/Execute_E_M_plot.Rd
5189347034ca7d58ab45bb7d4a13e371 *man/Execute_GSVA.Rd
dcfefa143c1f22b97924d756c20e9fc5 *man/Execute_GSVA_parallel.Rd
ff59a2e2397538c86d6d3e7487a0bb34 *man/Execute_JAS.Rd
9f30bf9907a914d654b5336c41319353 *man/Execute_JASMINE_parallel.Rd
f3d20665186dd102d45e2cb38b0a0e77 *man/Execute_M_dimension_plot.Rd
cc3b448cdbedb1f48b4351fa25bbb467 *man/Execute_SCSE.Rd
0db136a1f3caf198559f80c7587d009d *man/Execute_SCSE_parallel.Rd
1747f024acfc06622cca7ace554eebb0 *man/Execute_nnPCA.Rd
2bcb6ec7c4d6691cec1ea49f8632241e *man/Execute_nnPCA_parallel.Rd
c8c0883fbadc4f5f0fd9c7b7537b7022 *man/Execute_ssGSEA.Rd
044a15f0265d71b82860794df74642ab *man/Execute_ssGSEA_parallel.Rd
c31093800dd50fc8d768e88c87dc127c *man/GO.Rd
8e390b72b51bbc33a196202336eb4218 *man/MSigDB_Hallmark.Rd
428c658cdfb2047906e9003492121ad8 *man/Panchy_et_al_E_signature.Rd
b1e892a9006008849b35802505463342 *man/Panchy_et_al_M_signature.Rd
c685d84ee97d2d1f965ecc33c41a8a8f *man/SCSE_Result_EMT.Rd
76c9e977be0947186ae78329228d792a *man/Tan_et_al_cell_line_E_signature.Rd
82998bf275bb8744b704cec604adf53c *man/Tan_et_al_cell_line_M_signature.Rd
5a00f57f57798861009d9115ec79a05f *man/Tan_et_al_tumor_E_signature.Rd
2cbac6cb6a52313c382c83406c69236a *man/Tan_et_al_tumor_M_signature.Rd
30968baeb0101744466fe9dbea768a90 *man/add_EMT_score.Rd
4c89470eaf1e3f0d30bc5f61ed89d1bf *man/add_EMT_score_Bulk.Rd
dc8badbbb20d0d5cbace6f2bfc6919db *man/add_EMT_score_multiple.Rd
12e7ed5a6c0720b3bddf1cc2986f8c2c *man/cell_annotation_file.Rd
336ac402981632167b7dc23d37d69965 *man/compute_Signature_score.Rd
9fdeafb9434c1fdda54dec496ee7b8f9 *man/compute_Signature_score_SingleCell.Rd
f730b8e05ae7bdd42100f121b50609ed *man/correlate_sample_scores.Rd
37bb550db63a0a7e400d6bdb452a2285 *man/data_for_plot.Rd
0ba9cec99cd5f71736d631aabe21111c *man/data_prepare.Rd
abfb0cb63b1a8c663f804d6914eaf841 *man/figures/Figure1.png
730dc45fa6c0c7b8ef5a72dad63f3f22 *man/filter_gmt_by_reference.Rd
ee9b108f5aa339e5c18bc04a3f80706c *man/geneExp.Rd
fca2d1448b09fab79efe2a3ff02c71d5 *man/nnPCA_Result_EMT.Rd
b81a09786b7baaa848ca1ef71c616d86 *man/nnPCA_Result_multiple.Rd
a3e2aa25e7f7a89e46a3c3f94b426ab4 *man/plot_EMT_from_objects.Rd
ea2e29170c992341fd0b2dbc3673c25d *man/plot_heatmap_function.Rd
96377ead7c6b9c9a4675e99a9ddea8c3 *man/predict_cluster_labels.Rd
179edf40ad1fc34c3ae24b64aa3c07f2 *man/read_gmt.Rd
2d2c3b7301f34cea617d09e3a3c28ca4 *man/write_gmt.Rd
186c095ea3bcbecbcdf52b65d7e14d60 *tests/testthat.R
3a68aa28d2470bf6df12e5fe7c51ca94 *tests/testthat/test-bulk.R
d48ed133fea8f78a40bea9de8d802f0c *tests/testthat/test-correlate.R
30df0ec1e94e2d1efacb686abf035d59 *tests/testthat/test-data_prepare.R
4775ff87f85c7351b047892715dd6d3e *tests/testthat/test-gmt.R
eceeca7d6aab10c1fb9a9263163570c2 *tests/testthat/test-parallel.R
85fca2e7619bb4ad07d9b7add689584f *tests/testthat/test-plot.R
bdcaecad4f928ba59dfda420e97c7d60 *tests/testthat/test-scoring.R
4af7ca38701e6df60b008918a2237871 *tests/testthat/test-signature.R
d7f01087b858eea291d57be50c07592a *tests/testthat/test-utils-gmt.R
c73bb78d85df03c0b06d7ad2bcb7c01c *vignettes/EMTscore.Rmd
