5845be4870aef43b7643729a2cbdb24a *DESCRIPTION
f317f08143826c483d86579f67667eb0 *LICENSE
f62900881185bf1126a0a932702d798c *NAMESPACE
54973ef73574f52c70a95cd5c106d27c *NEWS.md
6c1029a27c77de34dcb7f9622738e676 *R/CatsCradleEdgeQualityControl.R
26d77827153b8539e353053017df8134 *R/CatsCradleExampleServer.R
72e2ef21c059053d7fc0b8e0d3d2dff6 *R/CatsCradleGeneAnnotation.R
8f7fc9f9e30013fee56fea5b5513a26d *R/CatsCradleGenesVsCells.R
f5c620e0d32acf519dd6f9cb27642e9d *R/CatsCradleGeometricClustering.R
03ef0c0739c43a571cd0ec7a3db5e215 *R/CatsCradleInternal.R
aa4d2ce7a9388fa203f2040a98de4bab *R/CatsCradleLigandReceptorAnalysis.R
449fd720ed9330d4ff2e60eaef4e6dcb *R/CatsCradleNNGraphs.R
12e887c8fb4335a07573267265528aa0 *R/CatsCradleNeighbourhoodAnalysis.R
a5c644b2af18f7b65a64e2932258585a *R/CatsCradleNeighbourhoods.R
92bfd8e53567affc53175cf3a343d722 *R/data.R
106f50dac82dd30ac992df870812f6ac *README.md
60a8de01e137518814f9b38b8665671d *build/vignette.rds
048009a970c88e8b5151b708f87923d5 *data/datalist
a2eb5a3899923a88ca6767432dbcd6e0 *data/exSeuratObj.rda
5b9357e740a39b3cb40ea21076674149 *data/humanLRN.rda
61890dbca9f6933d015188758f6e9793 *data/ligandReceptorResults.rda
18d5af607b0d4f86e4dfd8e8f467fa42 *data/moransI.rda
17d4324f5d2fc9130de639c27fcb349b *data/moransILigandReceptor.rda
ca206f13f1db6d175853c10faf0f8c03 *data/mouseLRN.rda
3766190a454e8fee0b3de3b9f4121125 *data/seuratCells.rda
84b55d59bbc9622555be9cca52f4502d *data/seuratGenes.rda
326fb26c28b8c7dcb7160b33f1689fbc *data/smallXenium.rda
b71b59237d8b4e96f5c454687f284945 *data/xeniumCells.rda
5c23aa629346abef8a10df9e2889a179 *inst/CITATION
d1ae9041d61f89ec6f9481bfab38b9a7 *inst/doc/CatsCradle.R
7e72a151616981e93cb0a8e00f342942 *inst/doc/CatsCradle.Rmd
d006e00ac763aca74630f254fe289b7d *inst/doc/CatsCradle.html
f4d25bc3fb14280091e3517ef0c31cf0 *inst/doc/CatsCradleExampleData.R
9a024656ed5fa655a72cee408be3f4ec *inst/doc/CatsCradleExampleData.Rmd
2df2fa24610b94bb82de9e63752b9fab *inst/doc/CatsCradleExampleData.html
0f7fe6779b02cb5f88f2bbe6a9a4e40b *inst/doc/CatsCradleQuickStart.R
e0b4662a68655a0ab0a853a8532cdcbf *inst/doc/CatsCradleQuickStart.Rmd
6e01a50d0b37a188c9b2cfd1641c2787 *inst/doc/CatsCradleQuickStart.html
7c30885cb65dabeb299e982d066adca0 *inst/doc/CatsCradleSingleCellExperimentQuickStart.R
4850a0cc9fc4d764b5891758ace3b41d *inst/doc/CatsCradleSingleCellExperimentQuickStart.Rmd
2c5938185abe1aaaa130c7381897904a *inst/doc/CatsCradleSingleCellExperimentQuickStart.html
e448bbec9fbd21918147b8e0ffc84388 *inst/doc/CatsCradleSpatial.R
452649b20703a7ad9b434168fc598bf6 *inst/doc/CatsCradleSpatial.Rmd
c9b79629ca6fb53eb970096f6959e4b4 *inst/doc/CatsCradleSpatial.html
d31341c5e166520cf724526d4089d986 *man/aggregateFeatureMatrix.Rd
6e75235d8cd99aced0ce169efe8eee67 *man/aggregateGeneExpression.Rd
2ef552ab3c42a912ce346f160f8593db *man/annotateGeneAsVector.Rd
4af929bc5ffb809b77a6eff9d516f949 *man/annotateGenesByGeneSet.Rd
7e980370ac4ee4f2b1aa0fd1f04769cc *man/annotateLRInteractionCounts.Rd
0a4cb6548758c54466cd8ad8b3bc4c97 *man/cellTypesPerCellTypeGraphFromCellMatrix.Rd
84ab3b74c648b2dd6b3d559dd15bffdc *man/cellTypesPerCellTypeGraphFromNbhdMatrix.Rd
f5cbf0fed4621f11c76f0a72334e8b05 *man/collapseExtendedNBHDs.Rd
5c62aa8451fce70f328c7a54615e11e8 *man/combinatorialSpheres.Rd
a45c4b61272ad7b578dd86dca4248489 *man/computeCellTypesPerCellTypeMatrix.Rd
9e383a99e9915de4b444b10677f417fe *man/computeEdgeGraph.Rd
132540ac8d2ee4b161775806ea018479 *man/computeEdgeObject.Rd
2eddc58bb3ff3c1d08b8d53a61b36021 *man/computeGraphEmbedding.Rd
f0263bc357ccb7429fd608d424f9f05c *man/computeMoransI.Rd
ff44f4f97ac8754b6e6b4b688f145051 *man/computeNBHDByCTMatrix.Rd
316690c5e2b3553a31fb7194b15abd71 *man/computeNBHDVsCTObject.Rd
1028c2a348fec4bc9426886458de9cb7 *man/computeNeighbourEnrichment.Rd
375db41cf02e807eca161579bca08cb9 *man/computeNeighboursDelaunay.Rd
608bed1ac21f9ca8d427fb932c377964 *man/computeNeighboursEuclidean.Rd
9288f13601d077eccb618cb9a5782755 *man/convertToLong.Rd
373696887c30e4771b2101e72ef69c3a *man/countLRInteractionsPerCell.Rd
7583a50d43ab96a91a098576f7b1a46f *man/cullEdges.Rd
2b0ed251b904f189f99017f566146ac4 *man/desymmetriseNN.Rd
9d9ab4dc46adf55eaaffaf3ae0577127 *man/directedHausdorfDistance.Rd
75c6ac530b7495a981d9cebc448635ea *man/edgeCutoffsByClustering.Rd
432052a5fced68dc8b066306e2fc8c15 *man/edgeCutoffsByPercentile.Rd
2f2df53ab7ddcab1491316f1fd680d6b *man/edgeCutoffsByWatershed.Rd
42719b4d148257786582d27139bd0eb2 *man/edgeCutoffsByZScore.Rd
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4edb932ae5c3f10af926c7d9f90b26b4 *man/exSeuratObj.Rd
e9266635ee87dd97aed1a46161dd0a76 *man/exampleObjects.Rd
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c8dc845200dd2b87cde00b8b1ed42ab0 *man/geneSetsVsGeneClustersPValueMatrix.Rd
75abf94155619d278627422ad00c8f90 *man/getAverageExpressionDF.Rd
4564c97753f5416692554b8eabd84be6 *man/getAverageExpressionMatrix.Rd
3da7bfe57c2f17730d511ab0e443fc58 *man/getBinarisedMatrix.Rd
1dbf19605c3d62f383ba455bb20f52f8 *man/getClusterOrder.Rd
aec70acdd4ee19379bcd1b6b1803240e *man/getExtendedNBHDs.Rd
5adce16b2dd315a76938d4db3af406c8 *man/getFeatureZScores.Rd
0419abe88dfe6bc51fb6af2f5379fbfa *man/getGeneClusterAveragesPerCell.Rd
997841f062c7c7c253af3eb9a546c58f *man/getGeneNeighbors.Rd
12934d7a83ce69d26b2e606c5dcee18c *man/getInteractionsOnEdges.Rd
48660416172c960cb3eacfef5813b4e6 *man/getLigandReceptorNetwork.Rd
c79a33198bffaef337bfcb0959f62a92 *man/getLigandReceptorPairsInPanel.Rd
9f387b01885f2b484ac3a870b69dc71d *man/getNearbyGenes.Rd
de9c2b7c436d5a39a695e24ec7ff8c7d *man/getNearestNeighbourLists.Rd
2d1fc8b5025f24a999d681848a30aed4 *man/getObjectSubsetClusteringPValue.Rd
f287e5a0879ab29d3bc6b258c9599334 *man/getObjectSubsetClusteringStatistics.Rd
300073a1da043a8d1ed649d7e1a73c3f *man/getSubsetComponents.Rd
404a8250543f2baf9759052e58e618ac *man/humanLRN.Rd
0a9b43c1a6944f7dbb6e25f71ba9358e *man/ligandReceptorResults.Rd
a139ba1cf8941cdac2e2ec479c313a46 *man/make.getExample.Rd
6cd5d4d6c5669fe882a31cf59d011f05 *man/makeLRInteractionHeatmap.Rd
f0c6d20a26610de143cc43fbf08bf12d *man/makeSummedLRInteractionHeatmap.Rd
413771b38179c8a88e1ea7cf2e8653a8 *man/meanGeneClusterOnCellUMAP.Rd
a1eda47c7db3ea39598f262512ea9973 *man/meanZPerCluster.Rd
e958f62b2258c10b9f61fea52410e133 *man/meanZPerClusterOnUMAP.Rd
f030c616aed329c6c0ecb89645ea47ac *man/medianComplementDistance.Rd
951c7141010cacf942f63da9f621035b *man/medianComplementPValue.Rd
dd29d27783e41521c520511551bec162 *man/moransI.Rd
f84f05ab83df455cf065ecb5f99f9386 *man/moransILigandReceptor.Rd
973a13ba0fa579e4a1af6e10ad9f2611 *man/mouseLRN.Rd
f6b70442e99042841e56f84688e9c2a3 *man/nbhdsAsEdgesToNbhdsAsList.Rd
3524b4a183570b93c2a09c2f84a7a9f8 *man/neighbourhoodDiameter.Rd
bce9045318874a15c79f1c4c289553ea *man/orderGeneSetPValues.Rd
0efad5cc780a2f00ec703193dbbab74a *man/performLigandReceptorAnalysis.Rd
e834c178e6742d928c59672aed55f969 *man/performLigandReceptorAnalysisAnalytical.Rd
815b1358da52a56d53e5ed537561a16f *man/performLigandReceptorAnalysisPermutation.Rd
2756f8451463122263fef40aea114bb1 *man/permuteColumns.Rd
91a4c536cace78a5444b7586987cb130 *man/permuteMatrix.Rd
a9fee35dd74507b9f19dc4d2d28b2578 *man/plotLRDotplot.Rd
8e33439e76473e969a253cc4a761c1d9 *man/predictAnnotation.Rd
52efbe993aed6dc130b33dcfc5cb80bb *man/predictAnnotationAllGenes.Rd
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a7148e50cd0d9edd843596a5ada668f0 *man/randomiseGraph.Rd
c137e67c084f5d0a6988423af706c487 *man/randomiseNodeIndices.Rd
552cce0973c181e3e4b20bdc617dda51 *man/readGmt.Rd
e9e917993b61aa04e72e7513a6046e05 *man/runGeometricClusteringTrials.Rd
4792f824da4a27c5a2bea065d4c277aa *man/runMoransI.Rd
99605c31ee1ee6a953974a7be2a85bcc *man/sankeyFromMatrix.Rd
8379c96cb2282e231553a36f8ecf330e *man/seuratCells.Rd
591847c1f9b5f798275ab21e5f0096b1 *man/seuratGenes.Rd
277d5b2ff61a6333d97af89247028be4 *man/smallXenium.Rd
d7a43fbabdca609d41de6ec04602cf88 *man/stripGeneSet.Rd
f122e08069a6c6dea1642087866a494f *man/symmetriseNN.Rd
9f0cd2a616d8f1f564973ff1552f994e *man/symmetryCheckNN.Rd
a418a42258243f538189e84e067f0424 *man/tagRowAndColNames.Rd
c6d77e4bea7805d70ece6f411da6f097 *man/transposeObject.Rd
982608629bab27a17cc88bd5ede5ba7c *man/xeniumCells.Rd
7e72a151616981e93cb0a8e00f342942 *vignettes/CatsCradle.Rmd
9a024656ed5fa655a72cee408be3f4ec *vignettes/CatsCradleExampleData.Rmd
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e0b4662a68655a0ab0a853a8532cdcbf *vignettes/CatsCradleQuickStart.Rmd
4850a0cc9fc4d764b5891758ace3b41d *vignettes/CatsCradleSingleCellExperimentQuickStart.Rmd
452649b20703a7ad9b434168fc598bf6 *vignettes/CatsCradleSpatial.Rmd
c4aed4cfda9942448c5d958712b524fc *vignettes/actualVsRandomisedPredictions.jpg
2409fb1b1fe18e05e32ad16958012ee4 *vignettes/hallmarkPValues.txt
b798cdbe50381af1e5c4feb2514f35ea *vignettes/nearbyGenes.jpg
