1672c469c4f615bc8a4647bd881a018a *DESCRIPTION
17667f07d22ffbe136a7c6bb7785ec9a *NAMESPACE
bc69352dd56d45d597295b34683973eb *NEWS.md
33ab89211c487ce4360a6d5e2b0a7b3e *R/DE_between_group.R
cdfc765bed8868a6321e016f2601482a *R/DE_between_time.R
e8ecda3e0d09fd9cf82ec6b13e1df053 *R/DE_timecourse.R
fee77a0a0a69fc6b94024ecaa2d62311 *R/TiDEomics-package.R
acdae81d9000e7ebbfcb09b81dfe7bb6 *R/WGCNA_input.R
7350736c90f05594e39ca9b9108c8d98 *R/WGCNA_module.R
76b65193cc9a0aca32d8a6b04139ff74 *R/anno_multicol_textbox.R
e958264c8583849d963db40012ff57f4 *R/calc_feature_property.R
a613d88ceb5ff07d5f887769c9b927e6 *R/calc_mean_sd.R
d567ff968c777995ec74029a5329f2fe *R/check_inputs.R
f3cb52f881640bab2401c56f58b0a5b0 *R/combine_tide.R
a9f1bea0e6df23d5b9a5c630cc73744c *R/create_input.R
d022c44ade24cb48961f72a773ec3f74 *R/data.R
77dd7bb752f255f3a71346cd22f813cd *R/decomp_variance.R
6399702ff8173c30242720a554235331 *R/enrichGO_list.R
d46c6928e7b6dce4ad6ab4106213ebea *R/enrichGO_rank.R
3244b2d06008021ea7e9b82ec21a8573 *R/enrichR_list.R
b7fd0bbe199ab95ec89f7285a91cb2ed *R/enrich_msigdb.R
4de0af1e2ae794709afa02bf000808f3 *R/enrich_utils.R
25e0ef28f1e3219bb9493889fb31f318 *R/extract_consensus_hubs.R
7d952bbae998a6d74ff9ea1ced4c94c6 *R/extract_hubs.R
605b635ec7d8bc2dd891491efe476d0f *R/extract_segment_trends.R
84140cb8acb4ac3823f43e10f307699c *R/flatten_DE.R
2044357f68d8e3e5802e748d9fc3c992 *R/flatten_enrich.R
cda84dd534c5fb26b20317b92af22654 *R/global.R
a730d1bd17fcd3997957e3809baa4c8b *R/group_specific_features.R
5bc4c3a47cdf4874c862d7129317f28a *R/impute_groups.R
6324c88e011efdd5b81adf730765ea76 *R/merge_groups.R
459344b8fddd2eefe59933a1050b9a63 *R/merge_replicates.R
959b6cd594a171ffe277b3009b473d72 *R/normalise_to_start.R
5843f5fc6fee99ccde40ab59a5781a47 *R/palette.R
47cc3557333252833e8b81dbbe33b1ee *R/plot_DE_between_group.R
1595855a1e134ee88a7a31b5de874dca *R/plot_DE_between_time.R
24eb32541e789b136a4d3fd05404869f *R/plot_GO.R
a2f5b3f07d8b0bbe0b42e308aa0a4c91 *R/plot_ID.R
ff4fd73d11111a6df0d1861c96324b8b *R/plot_WGCNA.R
7751438fd26842f171cec99faf98976c *R/plot_breakpoints.R
75ddf8b80c83a2ca96b6a7a6f6ae8273 *R/plot_cor_matrix.R
5bab91c029ad4e2de91dd317b5a80317 *R/plot_cv.R
54c3faae60a51dfded5fd1e5011f1c58 *R/plot_distribution.R
8f1befcd805586349aeab3538987e70a *R/plot_missing.R
ad7ce4552f452a5330cfc250a854fd6f *R/plot_modules_h.R
90d8cb4bb179325ab343b871cdf81154 *R/plot_modules_input.R
844170ddfba2eec648053c037dcd86a7 *R/plot_modules_v.R
a4e9e81444432e45f2e220090275ee65 *R/plot_pca.R
f0bc9de11ea8402491a073bbe776f838 *R/plot_pca_3D.R
eb8d13135a6397b1f86792bae698ab89 *R/plot_pca_by_group.R
21352383bef285eb8d2acd1e41e305dc *R/plot_scatter.R
964e28bc3fbf5fd14b04fcad11507426 *R/plot_segments.R
9ec1a8e6999ec7dcaf7f14bf9519a689 *R/plot_trend.R
115de9543f571af7424a5dbcff7411c3 *R/plot_umap.R
df35f572ed294702969a896fff0f9a6d *R/plot_umap_by_group.R
f700c7137220060afc6c2b00a7f7a37d *R/plot_upset_h.R
65b090a2207f0ef62107dab442cdaee3 *R/plot_upset_v.R
03123009271b78d95d03ee162cb0a98c *R/plot_variance.R
fa96048e88b858ebb4e9a0186e47e3b6 *R/plot_volcano.R
b8478df90b1686646c6f66b9bc7cf6e0 *R/prepare_WGCNA.R
5beb32fca49068412d28e9a27e4272a9 *R/prepare_tide.R
b3abe0fdf572c9a911c0ed298fa851e3 *R/run_Trendy.R
7120357ccdca12c7aa841e63ce70e841 *R/run_WGCNA.R
3263028b88486c711cd95a538f37b6f7 *R/run_consensus_WGCNA.R
c9ba0d1e38a0b972f5d9f45efdfd5ef3 *R/split_groups.R
2e49ac3284ba1c4b78e1fb59b2a7dc15 *R/summarise_Trendy.R
57b62f8e9f6d5690ab3fae845ba96eeb *R/summarise_feature_property.R
a4e2195df748ae5ea3b23a8be10d7baa *R/summarise_module_metrics.R
b830002fe59b4dfa951f2c6400afc971 *R/summarise_module_pattern.R
662ef31ff28b11e4205ed8305f09f4d4 *README.md
3020937a81665a2e800d16e241552444 *build/vignette.rds
0f70709cffad2fbfa7ec4f2cc2c641c3 *data/example_cons.rda
f4dfd74a92fdd6ed69a6ea92c3d9d9bc *data/example_go.rda
e5dfaa66fa17415abf0ae11db6a1c733 *data/example_net.rda
7049232f7f22abbab7875f1732d63db5 *data/example_net_2.rda
34dafb4fbb238911569d35e58ffe81a4 *data/example_obj.rda
d9e620bc237df4e829f17a120116e38d *data/example_obj_2.rda
d7f52d03fdff28895bb223d875b83d95 *data/example_res_list.rda
102bf4187ef11375b955981aa2d9a817 *data/tutorial_data.rda
9381157ab6eda31dff5cbbcd62c5190e *data/tutorial_sample_info.rda
b8f6ea917610e4d27c47831793c0a137 *inst/doc/TiDEomics.R
65ad54a6018c744ac77ba2ca4c4831b5 *inst/doc/TiDEomics.Rmd
7aab38eabd4e0ea6d3f9262df1ffe3d1 *inst/doc/TiDEomics.html
d09649cc1db2fa6df703b76d0e250724 *inst/doc/TiDEomics_multi.R
2e275ed6b3e550cb642bba1ca6f6ab66 *inst/doc/TiDEomics_multi.Rmd
2f065bc8ff541a9a3c6638426a983ab1 *inst/doc/TiDEomics_multi.html
ed0948a2ac4c0d40ece46521271c7e90 *inst/script/generate_example_go.R
8fe8517be3bbf235923b2c302bf9f05f *inst/script/generate_example_multi.R
abc9a9728531f094f8b45d9f7295b20b *inst/script/generate_example_net.R
6bb76e47f897da40cc205ce794223073 *inst/script/generate_example_res_list.R
466b3c613448411d572381d84b6e2cb0 *inst/script/tutorial_input.R
3ae91babad8a1b07cccf44b056d4437e *man/DE_between_group.Rd
b9324be7617bb29a1d64e7bb4f7d735c *man/DE_between_time.Rd
2244ae246e9f688c7fd2cc854bb2333c *man/DE_timecourse.Rd
2fffd335fd6d148a0edec6afa6782fe8 *man/TiDEomics-package.Rd
060e246f7c4360e3d956f7c733280533 *man/WGCNA_module.Rd
4251c98c241ff1553bcf186df35a9d9a *man/calc_feature_property.Rd
acd0dd31434e8adfe7fc91f0b7c1f624 *man/calc_mean_sd.Rd
9dc0be812a42b7df4291e8b529c3b632 *man/combine_tide.Rd
9166944b26ce64006b626036b3b388b6 *man/create_input.Rd
eee9f97578c45d455457ce99545271dd *man/decomp_variance.Rd
af36c3092b09a18ee3f6e0c38a2b0f46 *man/dot-WGCNA_input.Rd
7dbf2bf5a86914d575508fde27a7cef9 *man/dot-anno_multicol_textbox.Rd
78e25f0b413a367016fccb885b4a23b0 *man/dot-as_se_list.Rd
ad3364a759afa07a5afb51be14ad414d *man/dot-build_marked_features_anno.Rd
40fee19850c60450d9f8d4f8f0b974af *man/dot-check_character.Rd
a534f04c846dfef4e80f8e93b3efa62f *man/dot-check_df.Rd
f23618775799e60168a5398f777d7af6 *man/dot-check_df_feature_property.Rd
aa2301ce13d9442b1efdec2b267aed96 *man/dot-check_df_trendy_summary.Rd
7a3ae807a4e3202461a3fa1f0bb21304 *man/dot-check_limma_input.Rd
4cda4476020d531286d19092cbbb2b2d *man/dot-check_list.Rd
f64b5f6e307d4e5d2392af20264c0a3e *man/dot-check_logical.Rd
d8417daec56c1128e327258972865d27 *man/dot-check_nonneg.Rd
91704a6855a7273b795076845ec10fcb *man/dot-check_numeric.Rd
50a93cb48624334731394c590c6c6373 *man/dot-check_positive.Rd
9af00d8ce8e9b96ba86c443151dd03dc *man/dot-check_positive_int.Rd
cf30076e63d724864b1699639b121026 *man/dot-check_pval.Rd
c81e680f15e05bb7eb0eccf1a6cc0639 *man/dot-check_se.Rd
4bc55f9f5977fa17ecb9ded9b7e5896a *man/dot-check_se_has_properties.Rd
fa2fe69d0dd577da7e5236cb0316f299 *man/dot-check_se_list.Rd
226f3ceb2a2e50122601800fec8a5905 *man/dot-check_se_list_has_properties.Rd
81f7e146a5904bd5d564f6c63b4dd4c3 *man/dot-check_se_list_merged.Rd
9564b3669ae598501275f88b4c01aaeb *man/dot-check_se_list_no_na.Rd
799ec59504e44e5d3e49a5f260f5a16c *man/dot-check_se_merged.Rd
d92b4e9ea11913f14a794b7aa0169645 *man/dot-consensus_kme_scores.Rd
9a552bc3baf23aa8154f3f22dbd43d1b *man/dot-hypergeometric_test.Rd
7b7fed1907d94a6092764a778e9b09ff *man/dot-make_selected_anno_zoom.Rd
0c7a4b5c489effae9556c749b2e51af2 *man/dot-match_assay.Rd
7a465feb3ffb0b7b39622f385be27beb *man/dot-measure_multicol_widths.Rd
cf7359a18412318fd00731aa523e2228 *man/dot-module_labels.Rd
eeee4ffb9982a9d04d6200045fb75ef8 *man/dot-multicol_textbox_col_grob.Rd
99033652504107010c43e65e13b0f92d *man/dot-multicol_textbox_grob.Rd
5bf1c15a26d1c6ff43bebf6fdb59d62e *man/dot-multicol_textbox_layout.Rd
ddb71b98f5746253c6c75f95f11cc58b *man/dot-multicol_textbox_panel_fun.Rd
f19cb312e1b0da990ea58055622e377e *man/dot-plot_modules_input.Rd
886cda27d7bb7e7b81725107c96c5a26 *man/dot-plot_segments_one_group.Rd
31f89099b1dc9990c9e75cfbfa443518 *man/dot-plot_trend_multi.Rd
ef4ba81e57ae1ae82f11ea6f155e708c *man/dot-prepare_gene_list.Rd
5443f7a381f99afb59e287153d75a107 *man/dot-recycle_enrich_param.Rd
36cc9161fce765f0d639b1e2503f23b8 *man/dot-reformat_cat_terms.Rd
568907fa84cd9c102f98d4cca4e52f86 *man/dot-run_Trendy_one_group.Rd
ee90822c4d49a2c2a41f09437ffbb6e5 *man/dot-summarise_Trendy_one_group.Rd
0a64a10956e4976b411b109c5884920d *man/dot-textbox_grob.Rd
a029b9bea1db57b8136afcc75fbe0a91 *man/dot-umap_n_neighbors.Rd
5d747a5297b1d4e6c5b004fdc432d33c *man/dot-warn_unshared_features.Rd
081bb625baa518e851fdeb3dd586304a *man/enrichGO_list.Rd
d73d9db49e0b47c1d649ffd031842aec *man/enrichGO_rank.Rd
73787bca20c044a7ed212ecbb9fb8d2f *man/enrichR_list.Rd
546b00748258bd77ab649dbce85d7536 *man/enrich_msigdb.Rd
e15790004c47a9109f4c6158a9dc6401 *man/example_cons.Rd
01b844324aaaac84a0ed6b1031d92bdd *man/example_go.Rd
60bd1c319088648d86d95790d86d405e *man/example_net.Rd
6295c1496bc1610de74dcc5455c84253 *man/example_net_2.Rd
397c5c57d51b4b5b842f0be601481157 *man/example_obj.Rd
77abeadbf567ea4a0ded95ab543ba198 *man/example_obj_2.Rd
aee56c06ad086a96c09e2243c479753d *man/example_res_list.Rd
8fc4d4ba0c3e702580fdd7d39c143d22 *man/extract_consensus_hubs.Rd
87b043dc452f23a22a0936118c8f0ddb *man/extract_hubs.Rd
0fe97f137460260f571516383c536ebc *man/extract_segment_trends.Rd
6348b56cabe53d63f9b9c22969c8ab87 *man/figures/TiDEomics_workflow_v0.99.6.png
ef5411aaf3141109c9a0658df3448326 *man/figures/logo.png
80cda7e40b497a4e0ff73c5c1e863c88 *man/flatten_DE.Rd
f70956bd065548c9139354347ab64065 *man/flatten_enrich.Rd
ec5507381ddd045a8bca2e5657179602 *man/get_custom_palette.Rd
627d69231d8f3447bffea7ca4b84ad64 *man/group_specific_features.Rd
c5b76589df00d8493ea7d5f67378f276 *man/impute_groups.Rd
5a6034354569ccdfbf85552237e5a53d *man/merge_groups.Rd
344ee4289d41d7171d062a7eea2f005c *man/merge_replicates.Rd
d014c6e8a0c80b1dfcc2f2e995534a4e *man/normalise_to_start.Rd
eb56467cdfe36b61c81c39751eaa5d38 *man/plot_DE_between_group.Rd
50cba9ad31b17c6ca1867381d7b8c77b *man/plot_DE_between_time.Rd
22001ae88b1aae300a881a473ab56be9 *man/plot_GO.Rd
95f5770da16a269612dc03b6ebe14b25 *man/plot_ID.Rd
f40e99d79fddd72a8b6796cb55040bdc *man/plot_WGCNA.Rd
4defc6ec59b2a97b9f481bb439e88523 *man/plot_breakpoints.Rd
b8a613f21777f30313b3ad266846cf61 *man/plot_cor_matrix.Rd
d2d8d061b8e2288c07b0e8c9f7d563cb *man/plot_cv.Rd
d7c1e7f89dc951483cfe5bda74b480e7 *man/plot_distribution.Rd
4fe4a2662b3967030685a5a5ea2589ec *man/plot_missing.Rd
bfe866ce36bc7333bb314917c39a40a5 *man/plot_modules_h.Rd
18ebfd334ef64534846774540662b284 *man/plot_modules_v.Rd
98793b75ce70809ed130016fd5da06ae *man/plot_pca.Rd
fae73d83ceb4e596d80770c75979ecd2 *man/plot_pca_3D.Rd
58ae577b749798c05732b24b1f083524 *man/plot_pca_arrows.Rd
9bb5c92716484480284f620545c94943 *man/plot_pca_by_group.Rd
d85e2b803fde9fe2c2f74c027fbb309a *man/plot_scatter.Rd
b82a3efefb90a10b4448d791ba1d5f2d *man/plot_segments.Rd
669557e0671909cb26f6fe16dbc9e7a4 *man/plot_trend.Rd
2708dce4e4a428dd2b37fec2844b73d3 *man/plot_umap.Rd
f039aeb42951d4effdb4e52e60ee8393 *man/plot_umap_by_group.Rd
599f0882b10d72645d0fca4a34760c6a *man/plot_upset_h.Rd
8acd282827b3584f230806aa85e682f2 *man/plot_upset_v.Rd
3319328348d4089b8e473c186d571adc *man/plot_variance.Rd
329824317bc88f0f4254deb17c0c81b2 *man/plot_volcano.Rd
51af50995921eb4757e80b4db964b7da *man/prepare_WGCNA.Rd
740f16d201380d902c6cd9d09bfef53a *man/prepare_tide.Rd
6eea8a10e0f86facf64dc766882f3ff1 *man/run_Trendy.Rd
65a825da6eb4c6f601112dc2a66578d9 *man/run_WGCNA.Rd
52e123533c0c4fd869a0f2747c0e8bed *man/run_consensus_WGCNA.Rd
c185c29ae922974e8cf15bc7ae71f704 *man/set_custom_palette.Rd
2290dfe792104363f465bcff06497cd4 *man/split_groups.Rd
f7b12746897d3ad50599cc3769ae927c *man/summarise_Trendy.Rd
ae8f9b56f4d7cf0045c7125edf9f519a *man/summarise_feature_property.Rd
843dcb65bf2c9493a23e973672d66c06 *man/summarise_module_metrics.Rd
293568b8226fd3d348628c86cd2e664d *man/summarise_module_pattern.Rd
1eb1eab645edc88977976683c66d761a *man/theme_custom.Rd
5dd082b97bf05f75568b0a2bebc90bd0 *man/tutorial_data.Rd
db2ae299e7e50ed861929be16c8a05dc *man/tutorial_sample_info.Rd
3db0e4a7e5a6c5415da5eef7412a3440 *tests/testthat.R
8eaba3d62bc12ada146deb94e005d5ac *tests/testthat/test_WGCNA.R
03d4f0c33ac6af480b8e0d5089da0aea *tests/testthat/test_WGCNA_multi.R
34dc92d160c1571b68fdf7ed5d39218a *tests/testthat/test_data_prep.R
20ac528b39e722bf76b032f5607a4a30 *tests/testthat/test_dde.R
dd582022323579710f9496f3c0ba75de *tests/testthat/test_enrichment.R
19befbb009103170828398d76fc69a1a *tests/testthat/test_extract_hubs.R
4c20ef1b810b2207f0f67f9fa07c27be *tests/testthat/test_feature_property.R
0b1253b3e30956ae8af7922942bce089 *tests/testthat/test_merge_groups.R
5156886fcabab454e06071b0d6628143 *tests/testthat/test_module_labels.R
0013ec8568e1e49f41b6e48edbbd4be3 *tests/testthat/test_msigdb.R
1b143ca43c31b17d063f7647cb252827 *tests/testthat/test_pairwise_DE.R
cc173bd018ecb7c95a252935e1651630 *tests/testthat/test_plot_modules_h.R
314b0b6411ce72f83faf0911475b61ca *tests/testthat/test_plot_modules_h_added.R
22fbfed8143d2936fdd87146ce508d01 *tests/testthat/test_plot_modules_h_multi.R
56fbffad01df956847f01fa892965461 *tests/testthat/test_plot_modules_v.R
974818fb5ef428459146ae59f5bac50e *tests/testthat/test_plot_modules_v_multi.R
4d25d0f66d9f11bb1e6029ccdee5bd3c *tests/testthat/test_plot_scatter.R
32ad4a2b6e66f8a605dba7f744bedf40 *tests/testthat/test_plot_segments.R
9480f226df0473f011c6b42c01793acc *tests/testthat/test_plot_upset_h.R
df26beacf05981e146089a44af82f54e *tests/testthat/test_plot_upset_v.R
7dfb0bd3586fc4224dcd07af99a46427 *tests/testthat/test_plots.R
6edce6bee758623cb7062d0d2ec04f45 *tests/testthat/test_plots_multi.R
6903159575c7500c48f57e0be1d3beb5 *tests/testthat/test_subject.R
696ed5cce613ace174910a0ad8675fb1 *tests/testthat/test_summarise_module_metrics.R
0e99ed671bde5dfc15ba15f133bfff5c *tests/testthat/test_summarise_module_pattern.R
925ba50f65d0d4352abe8c5084b4007d *tests/testthat/test_textbox.R
b1f3bcd4d057bec829e6e3eb15da5958 *tests/testthat/test_timecourse_DE.R
7af1482082284edfb5238758e28ad001 *tests/testthat/test_trendy.R
f6a386c56b1665d55cdbdce4b43e5d13 *tests/testthat/test_utils.R
b4babebc9de449b9b48af988d8e482d1 *tests/testthat/test_validation.R
65ad54a6018c744ac77ba2ca4c4831b5 *vignettes/TiDEomics.Rmd
2e275ed6b3e550cb642bba1ca6f6ab66 *vignettes/TiDEomics_multi.Rmd
612ed61c580a4c9883679d121ec71406 *vignettes/references.bib
