5127ba58f1c959ebdcb32c37dedcfc56 *DESCRIPTION
2618146374e9e69c50452ae8b5856325 *LICENSE
e7147ad108d21a5dc36ab1abfbdefb97 *NAMESPACE
22e756404f01d48a5edd00959becfc73 *NEWS.md
a0cc16e979ee980b890f4b44cc6a3b7e *R/assess_pair.R
e2871a0e43126997e43a46a586c7f0f2 *R/coexpression.R
e0417be2afce01500daad00cc4651255 *R/compute_metrics.R
8562778da18a6f42bc03922bff3d889a *R/cross_celltype.R
cac8344bedde19a2265b7a4c3a63da4f *R/find_all_pairs.R
a7ef5cc86ce2a8b274d4de3a1349ea5b *R/find_gene_pairs.R
bb526b864438ba681e48c6a8be4db415 *R/globals.R
329788aab5accca237781e124178a3c6 *R/neighbourhood.R
cf0495565917daaaf1345f4ce72f6e10 *R/onattach.R
6538bb4c19018df4db3de6edb7729d8c *R/plot_cross_celltype.R
38e0aca55c1eed84fa6bac3315fda191 *R/plot_heatmap.R
b02850a222dbd247742d97249df472f6 *R/plot_network.R
c304331bdb5c18d7c6ebf69b3bcb5352 *R/plot_pair_dimplot.R
4aa6ab80f2abaad3a9ff9d752e9a944c *R/plot_pair_enhanced.R
19bd2db5cd0b34572af08d62e81b6790 *R/plot_spatial.R
14beb4dfa46355ed87050e3b3e6b8e91 *R/plot_synergy.R
f3e97521bee9e0d507e76a11f59ddce9 *R/plot_utils.R
1793268a8c5c02229f7ace1893596fec *R/prior_knowledge.R
f7238415b8c561c1846e74db2a9eac0c *R/schema.R
2a41e9e3f084db1bb4bdf200551ad338 *R/score_integration.R
8ecab318385b43bd77dbda8dca594832 *R/scpairs_testdata.R
1a035d21ff3a461b147cc8d9cd44a7bd *R/spatial_metrics.R
dd8b382c9b3ef31678472b8620463329 *R/utils.R
41c4ff11678b2589ca1c660038052015 *R/validation.R
ae3bad293bed1f7eda80c8a252d2b986 *README.md
7b1aed510328656243b63456a8bc3d40 *data/scpairs_testdata.rda
3797a57cd91e6a1af080f935a3586ac1 *inst/WORDLIST
0b54de9b72eeac19f76e058bfc455e96 *man/ABS_METRICS.Rd
b851e67655ce14385adb77ba150bf7c2 *man/AssessGenePair.Rd
2cbd9e93f50112a0aed50d783f7a405f *man/CONFIDENCE_THRESHOLDS.Rd
ff4d16d447938418e978f0330b27f0e1 *man/DEFAULT_PARAMS.Rd
5aaf8b3bd4e94181f2348f7f2f1a432a *man/DEFAULT_WEIGHTS.Rd
c77bc77307b50388ae42fc1d7e1cb7e5 *man/FindAllPairs.Rd
dce1e2eaf15ff9fe183ae6405709b888 *man/FindGenePairs.Rd
c8db713767bcc36edd721ea8f6e39c4b *man/PlotBridgeNetwork.Rd
5fa23f3027ccb3144d63f1547dcc4c40 *man/PlotPairCrossType.Rd
0f7975f672bb6be6635a02d376389ea4 *man/PlotPairDimplot.Rd
bad3bd09d5858de78f567ee39962e8b8 *man/PlotPairHeatmap.Rd
1472d7f206111e7ed21c5839e6f0dde0 *man/PlotPairNetwork.Rd
f392859e8a650d177b5fc59f3b468035 *man/PlotPairScatter.Rd
f19bd0f95a27d48f6d76da994b403372 *man/PlotPairSmoothed.Rd
77ffa5be0f43f7f81f802bbeecf10941 *man/PlotPairSpatial.Rd
34e15e8236897ac9ae53857d9f711e34 *man/PlotPairSummary.Rd
f2aac816841563ce252f8dde17e0d4dd *man/PlotPairSynergy.Rd
9144ad9808f6350bf6d9bf02e367976c *man/PlotPairViolin.Rd
740fc6a1e39903e6fd6121182bc292da *man/RAW_METRICS.Rd
242da86344118426978e4fa1b221a843 *man/RESULT_COLUMNS.Rd
624d83cc990fe6a5c5e6f069ab63ebfa *man/SCORE_CONFIDENCE_QUANTILES.Rd
4e738d5cc665deb6a2c9a4e600204e83 *man/cross-celltype-metrics.Rd
54f13fc572f04f969a96704d0f03a6be *man/dot-align_spatial_data.Rd
3ef4725ba03f11debdc3df6d5e779a7e *man/dot-assign_microenv_bins.Rd
68a096abf28f4d33a0c01c2f92efae11 *man/dot-bicor.Rd
393ced2904b85eef141f81e637ad19f8 *man/dot-bicor_matrix.Rd
2406b25099d13bd4658443031e229876 *man/dot-bridge_score.Rd
cc0d5f0b60ec2c971806f1c51eab0998 *man/dot-bridge_score_batch.Rd
81fc787d557cf877f77656fd26e5e8f5 *man/dot-build_heatmap_panel.Rd
f2c462d49ba24007632a69135dd452dc *man/dot-build_knn_graph.Rd
c6d22a3884d21a575bdb749688af2f61 *man/dot-build_panel_theme.Rd
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b5df972f81234ec1203f764cb86e4a3f *man/dot-build_result.Rd
ea557b24e4ce9acdcbb571ee124ad35c *man/dot-build_spatial_knn.Rd
a71ffb09dbc314ef2b2c8cea4fa06dbc *man/dot-cluster_cor.Rd
80f913e5a63d94cc7ca4e3f410c287c0 *man/dot-cluster_cor_batch.Rd
83af1fbde9b96e9e298e5788466fef0d *man/dot-compute_bicor.Rd
43cbf78ffc07b898c6b4a66a4f9ef036 *man/dot-compute_cluster_cor.Rd
cdc64a93ab70c51d14eee0879dddfc8f *man/dot-compute_coexpression.Rd
f74387ca45a52d7fa9a92b4aa0f294e4 *man/dot-compute_cross_celltype.Rd
7142dc7be8a9e53a5b7d275b677d9008 *man/dot-compute_mi.Rd
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ddea56c9bc46c32d2bec26020aa67f99 *man/dot-compute_ratio_consistency.Rd
2a9c29ce7942ea330dddab2660ebe499 *man/dot-compute_smoothed_cor.Rd
4a47f9712eda03475ac9776a4395e3fd *man/dot-compute_spatial_clq.Rd
ac1b604faa5e1f7bd47dcb51ec8f4597 *man/dot-compute_spatial_lee.Rd
45f50b035556267e34f82c16355d5ec6 *man/dot-cross_celltype.Rd
f3cd6d349babef3b5f4e82146efe7307 *man/dot-cross_celltype_batch.Rd
e95fa14aa4032aa06636ce1bc07ada18 *man/dot-cross_subtitle.Rd
9b180235d1d7fed708ea9d751d43aa3e *man/dot-extract_pair_vals.Rd
4e9db2ab0f7531219f0e857e671b8ea1 *man/dot-extract_pairs_df.Rd
be24244e6da60688512783879b2b444a *man/dot-get_expression_matrix.Rd
f6c348628ff7ae024b6c53549dc40554 *man/dot-get_go_gene_sets.Rd
80c04556fc58a65e629844ff569e0e27 *man/dot-get_kegg_gene_sets.Rd
70f075d7865641c0844d4fca2d866602 *man/dot-get_spatial_coords.Rd
d3da9cdc64978b602c505bbe8616395c *man/dot-has_spatial.Rd
73083ddf5d795f1da3a80e8fbaff169e *man/dot-integrate_scores.Rd
3e9db22a60a1316c440b3e191e021ee1 *man/dot-msg.Rd
9ed65d73de065a434331366d5646ac14 *man/dot-mutual_info.Rd
f281bd4316ccdbf6d058122e42ab0955 *man/dot-mutual_info_batch.Rd
5030eaff7f5fdea177772ae7bfeefddd *man/dot-neighbourhood_coexpr.Rd
9d272967a9bcb909c6e3ca7fc8951d94 *man/dot-neighbourhood_coexpr_batch.Rd
66ee1d6c8a78e4fa947d2247e374e336 *man/dot-neighbourhood_synergy.Rd
ca7996d86bd06ab833cbc04ec42de319 *man/dot-neighbourhood_synergy_batch.Rd
a0bf93e394b88c84de5f9fa15a6ba6e5 *man/dot-plot_bridge_network_enhanced.Rd
b5990afcdde1005b775c6b62391d2014 *man/dot-prepare_expression_data.Rd
45397fc6cbd6f3ff4c5692f589e564a7 *man/dot-prior_score.Rd
589baccfd577ed15aebbd1146bcc8509 *man/dot-prior_score_batch.Rd
6c395a26ded8fe5b9ef9bdd202e73661 *man/dot-ratio_consistency.Rd
d43cd7dc72115532cdb2ee21b12a2282 *man/dot-ratio_consistency_batch.Rd
868749d6016ea684566c7c17e832b1f3 *man/dot-resolve_cluster_ids.Rd
702ce810146407c05e0f959cde6d0b4f *man/dot-row_vars.Rd
b159e10191ec883842986c831439dfdf *man/dot-select_features.Rd
b979aa73519e49aa937f656d0757ed38 *man/dot-smooth_expression.Rd
85716a8f27762674e90c93ec3af58aa0 *man/dot-smoothed_cor.Rd
c23b6b41dbbd89687459d5068b9224ce *man/dot-smoothed_cor_batch.Rd
0730bb7ee1168b93e5a939829c8e75a0 *man/dot-validate_binning_params.Rd
14dc0516a450421029b70c2ddf4638d2 *man/dot-validate_cor_method.Rd
33d2fa51aba4fc3561d7f9dfb0e7c1fc *man/dot-validate_features.Rd
3439797665403e4a9402366a836690f6 *man/dot-validate_min_cells_expressed.Rd
34dc1050b4d227b7e01c5e156eef2749 *man/dot-validate_n_perm.Rd
7f05fe360046aa9292a83a129a8e8f08 *man/dot-validate_neighbourhood_params.Rd
ffe5e636bd17030f2a231fae2e41bfc6 *man/dot-validate_percentage.Rd
b7f124a703bc438144d4a4ea85b62491 *man/dot-validate_plot_inputs.Rd
60ad7c5fd26d8e5c62f3ef81420e5009 *man/dot-validate_seurat.Rd
5ecfae79768be21ec1bc607a503ca17a *man/grapes-or-or-grapes.Rd
b9efde75052afc5c400a16db788b23e0 *man/neighbourhood-metrics.Rd
dc066793932ec8968ac341311efc85d6 *man/plot-utils.Rd
5aa69c65a0170754282baae476827c1b *man/print.scPairs_gene_result.Rd
060e4924d265e247450ae20bcff76de9 *man/print.scPairs_pair_result.Rd
44b5e8a1f46cf52544543d91b6a9f70d *man/print.scPairs_result.Rd
4bee5db8292ce6810a3df4624431f772 *man/prior-knowledge.Rd
831af31e4f4ea6fa9772782b867017b5 *man/schema.Rd
90adf020a7013989773e2e6fbd2f12c0 *man/scpairs_testdata.Rd
4478100e42ee7363bc67225faf95d872 *man/spatial-metrics.Rd
9473ed818b6ba5eb69de7c3cd94e84c1 *man/validation.Rd
87d2192ff0f9deb1c4f5992a5856907b *tests/README.md
4763486eb54c988f67b4cc8c549fde57 *tests/testthat.R
5379e870ba6195d8df360331afe9ad20 *tests/testthat/helper-test_data.R
3cf0c3a93158e36aa3f6743f5db6c035 *tests/testthat/test-assess-pair.R
ebd1151f6d286138029cad23a440c404 *tests/testthat/test-consolidated-functions.R
e5ee7a770d7551af561773fae72c22c5 *tests/testthat/test-cross-celltype.R
cdd26fdc0950ed4b2df34f1ffe49bb15 *tests/testthat/test-find-all-pairs.R
597350e0eeb2f7d6d857207f031cde18 *tests/testthat/test-find-gene-pairs.R
d2dbc5868b2d1b271e8463ff8c3edd60 *tests/testthat/test-internal-functions.R
7653a25fa4ec12d0609a39bb9d281294 *tests/testthat/test-validation.R
