25cec1c7d4af828dc329dcde270c92f0 *DESCRIPTION
84dcc94da3adb52b53ae4fa38fe49e5d *LICENSE
e1cad623d30f7453b9f244137b898f18 *NAMESPACE
73b0b9aabaf90146055c3077f90f1739 *NEWS.md
ea15161b9e31643ba36c54b12ff7ba54 *R/RcppExports.R
4d3226f77f518b70a0f1284888305aa7 *R/clustering.R
897d4f029968ef719f3f560379efa648 *R/convenience.R
67fc51b953bf3c68448b7c97c9a54e0c *R/data.R
bd7e250d8e0251fa0f7d79ed441b284a *R/differential_expression.R
53349e3e1d4f717873c69c1bf27c1901 *R/dimensional_reduction.R
ae9f7966044d53426f895dd1294b388e *R/generics.R
8826129b3d95e2c810f93ab9e1a6cca2 *R/integration.R
0f730c19148c54e4f657b8db050c571b *R/objects.R
a1ec966286277ef3ee0fd8c9420f6cf9 *R/preprocessing.R
e3edadd1e8bca42f3e72a8af1e2a1f66 *R/tree.R
9efb9a83860da570852b643bc6277106 *R/utilities.R
dc04827429d055f7399f3a74b82c4622 *R/visualization.R
2ad9682105a1eb97d72598e8b786508b *R/zzz.R
e8faf9dcc4455b9ce6d30e538ae9ae96 *README.md
e84661f995a9f29d1a09ebcdc27d3a82 *data/cc.genes.rda
55d7e35793436d5e91646d774d9f86c4 *data/cc.genes.updated.2019.rda
f31fc6d89626ed493ef21557a33021ac *data/pbmc_small.rda
f8e3f10318a2bc7bed0d5db84022376e *inst/CITATION
d07fe4eee5c09cc44e96c17e683cb10e *inst/extdata/pbmc_raw.txt
92399dea30b73958e8a73e9bd64fe7c1 *man/ALRAChooseKPlot.Rd
810b7f6f7e75549233f36b71b9a294e9 *man/AddMetaData.Rd
d5e72d9a30865188e0d161bbec716621 *man/AddModuleScore.Rd
e14f943a4f877f848967b0167562c071 *man/AnchorSet-class.Rd
4709dbf3a30bbc41892734b4ac0a906e *man/Assay-class.Rd
03b2b97088e383fd8a6e6b261b82a5d5 *man/Assays.Rd
afa2ca7ee28cdc822add9aebf459f253 *man/AugmentPlot.Rd
c3133d7441564c1b62256039f650840a *man/AverageExpression.Rd
d9558f568959bfbd8024fb63642bc61e *man/BarcodeInflectionsPlot.Rd
11dec462d0fb9f53b2e2dddf22901577 *man/BuildClusterTree.Rd
e4b663345d84c3187146813de0753a6f *man/CalculateBarcodeInflections.Rd
8ce765eeaa066c7a1d57dd3b5dcdf366 *man/CaseMatch.Rd
5f6db66903af4a920834a896d7b6f45c *man/CellCycleScoring.Rd
976caffa5a22837dcd9f86bacd89fbf4 *man/CellScatter.Rd
295a7d839185b68bf925e77fa58501ca *man/CellSelector.Rd
dacda2e4537d0e4235380a301153c6be *man/Cells.Rd
f30ff8d9b4233dd5d7e61eb9689504b2 *man/CellsByIdentities.Rd
af8d5176d4a46599e4f5823ea613f653 *man/CollapseEmbeddingOutliers.Rd
0089998dbf3b9ceda566902225a44857 *man/CollapseSpeciesExpressionMatrix.Rd
ad99d2e4290503f1607168de24675426 *man/ColorDimSplit.Rd
e734784435ce40c180fb4519126c20fb *man/CombinePlots.Rd
48df91074760789c3bf9285b472303b2 *man/Command.Rd
daeebf2d27175e0dc2686b7be75c8767 *man/CreateAssayObject.Rd
274d5ec0859d6ea3c7274e2bd8589e9d *man/CreateDimReducObject.Rd
3fbd05c4420b9b125411fedcf2832833 *man/CreateGeneActivityMatrix.Rd
1da7d55b87a11f0e61eba56b47b01035 *man/CreateSeuratObject.Rd
ed3cf6431b7ae74072711f5cdceea03e *man/CustomDistance.Rd
f00401ae93dbb69d80ba0e187b8d75fe *man/CustomPalette.Rd
8bd4eefb1a4a89ff91ecefc176bfd639 *man/DefaultAssay.Rd
3d674ba31ef6ca856ae51bf91490cb8a *man/DietSeurat.Rd
ca8d16b70226824e358a290e72190041 *man/DimHeatmap.Rd
264b24df7505cedcb39acbc46a38d014 *man/DimPlot.Rd
2df9fdad586146228cd52ca32c085f2f *man/DimReduc-class.Rd
6129b2dbdc749ed2880a2347ab3f01a2 *man/DoHeatmap.Rd
5464da2a0d43ec9806c0744cb6102b6c *man/DotPlot.Rd
7f990b57af606c619cd32fc4823df3ba *man/ElbowPlot.Rd
2a9ff1776069af7481ae99b98ccd44ea *man/Embeddings.Rd
bc95170ed6c7905738b758a0501a66bd *man/ExpMean.Rd
f135b57ab61fdc61c872995c053aee5f *man/ExpSD.Rd
e5f8196d5bf616784532f3b91fc35b9b *man/ExpVar.Rd
473bbd37b3b88e75f683e562dae4e82c *man/ExportToCellbrowser.Rd
3f86810236bdb62e20be6be6be1269bf *man/FeaturePlot.Rd
104240e8fcc9501065c1e8e0b77e2691 *man/FeatureScatter.Rd
6aa7b60217d27dcb3269a78aa8157794 *man/FetchData.Rd
2e6cbc0e4a80844dfabcd467b16e8994 *man/FindAllMarkers.Rd
69f2d076dcc5a2dbb712ad9c0093e161 *man/FindClusters.Rd
2ed0894c70d245789f61bd5945d6e805 *man/FindConservedMarkers.Rd
203055e6abf84de27003f4f742f54735 *man/FindIntegrationAnchors.Rd
4e7b7fb661e7e76dbb59a999c1a0483d *man/FindMarkers.Rd
0956b1358f1e7fa30525c2ff4dda0866 *man/FindNeighbors.Rd
d0a7d5f6d9170252347d0847f83f86e7 *man/FindTransferAnchors.Rd
cc7606bba42dfc8e7ead5677d2a36a38 *man/FindVariableFeatures.Rd
0510c94030d8033d795243dcea889310 *man/GetAssay.Rd
4b28e1ae9e34d811ba9b93a434f82cb6 *man/GetAssayData.Rd
8c67742b1850e245dabeb0080496092d *man/GetIntegrationData.Rd
5bda2b861e1c36962e51c08299bef239 *man/GetResidual.Rd
ffcc1c8f1aee243053d55e54b026fc28 *man/Graph-class.Rd
40aa09e4e94bebce4233e69bb943823b *man/HTODemux.Rd
6969cde8f2969dce156d94e9ce5dba51 *man/HTOHeatmap.Rd
e095fe2a13e20bea7fb8c5850ede332d *man/HVFInfo.Rd
e342e4ec0066bf6139aefd02ea29f90e *man/HoverLocator.Rd
e2e777e9d8f88face9586e7b0ea44d1a *man/Idents.Rd
f52c31c7f64881c8c16fbacb09a43e58 *man/IntegrateData.Rd
f07f85f35c068862949ba8aea6a7d0c2 *man/IntegrationData-class.Rd
ec33d0c8b0a12d18edbe74c50e6b57c5 *man/IsGlobal.Rd
b577e19ed30fed4dad88521ee8bb5f3a *man/JS.Rd
4a9224370cdcdcf924a2305c5f4afdb6 *man/JackStraw.Rd
7032df72bd3bc5bf505aeb5404ebe736 *man/JackStrawData-class.Rd
6f1773e316b1e47022bfffb082bb4700 *man/JackStrawPlot.Rd
419378df10e1776c68fc8cac800442e0 *man/Key.Rd
ec6e773d7bccd1b7fac4f4f775b8434f *man/L2CCA.Rd
7d827c4056462d47b10ee51135b81a28 *man/L2Dim.Rd
b589c5578bf5cdad033024e3ad0d958a *man/LabelClusters.Rd
e2af95bdbcef934a02b5598c7afb832c *man/LabelPoints.Rd
c86833fe9142925715f6a86ff9b69929 *man/Loadings.Rd
cf47ba5b026ce195c22915397d1cff5e *man/LocalStruct.Rd
27dfb4f34c7026afcd9cced076173e10 *man/LogNormalize.Rd
6abf43f5649e3dc037f802111fb92f00 *man/LogSeuratCommand.Rd
19f058751ff474965ebcc796ac7dcda4 *man/LogVMR.Rd
b507315c5715e5f1b8082680424738a5 *man/MULTIseqDemux.Rd
d3aa14c39bc65a8abe135b4ee92d8688 *man/MetaFeature.Rd
ad9c49b3faf112a1882eb0c009547070 *man/MinMax.Rd
d096fdd966337afb93c9bf5253d791c3 *man/Misc.Rd
2e22e7fbdbac3d589af1e2c16f08b2d3 *man/MixingMetric.Rd
04ca10964c6bc1ac0146d2ab9596cd44 *man/NormalizeData.Rd
52d93fbe103f84e6083528ddf782c214 *man/OldWhichCells.Rd
79e9c1c27d132e64b663f3e34e9c9abd *man/PCASigGenes.Rd
1efea330395c0564b2f0ae6e22a78adf *man/PercentageFeatureSet.Rd
c472a070ae7e3777ebc2c400455b98b2 *man/PlotClusterTree.Rd
321f3abb712ca201853337d7c12577a7 *man/PolyDimPlot.Rd
7e37991b1c3e5aabfad83b4bb574064b *man/PolyFeaturePlot.Rd
3f561145dee87dd6da8aad816108bd40 *man/PrepSCTIntegration.Rd
803758cb5762fbe127063d8b089bcc1f *man/Project.Rd
5ee286d8fe64ea816e561b1ccf20d2b3 *man/ProjectDim.Rd
bbdfbcfd18329e0adca953a727edcbb7 *man/Read10X.Rd
bfa85204a7e639af961c8b0dc32f5309 *man/Read10X_h5.Rd
56bb82d14a62ba66da1a59c49d11b08e *man/ReadAlevin.Rd
b56201e48e7bac211cf4554073c5a05f *man/ReadAlevinCsv.Rd
4204fbd5b5b3e65a3b72b0037610dce5 *man/Reductions.Rd
9b9626a4b0c7b9c9ef9fa6e05a7bfccb *man/RegroupIdents.Rd
014f151148585ea420d641f6607b8866 *man/RelativeCounts.Rd
4c28028d3117e3e65c3bc8b321340452 *man/RenameAssays.Rd
cf5b888d70b3a678d49c83fded19f25c *man/RenameCells.Rd
74cd35fc5c37e33e49c6a7669784e99f *man/RidgePlot.Rd
9d88515b0807a289957c628cff8ff9f8 *man/RowMergeSparseMatrices.Rd
890f2b1e783d9402890ecf5186fe9e06 *man/RunALRA.Rd
f9ab831e5faadd46649fca01059359af *man/RunCCA.Rd
8379c2e1f9866bbac3a4d97d886bdae2 *man/RunICA.Rd
1d2b58092c3c4152aee376af9d47eeb4 *man/RunLSI.Rd
b9cab840e20365e383153bd8355564f5 *man/RunPCA.Rd
40247940f37d96ed7c98a6e7b5ad1893 *man/RunTSNE.Rd
dac1831717ae8df2f8aee9713662019c *man/RunUMAP.Rd
661328fe7a9dbbd7e14600c3f70b1106 *man/SCTransform.Rd
b92204c9406eb253e2e2cb4f6e980cfe *man/SampleUMI.Rd
5a0eb0a93e23effb1f3ee0425ed51663 *man/ScaleData.Rd
fd495007cdb81cd41818e09445a3e088 *man/ScoreJackStraw.Rd
9d6ed3c848f3bdc7a56d17442b4afa1f *man/SelectIntegrationFeatures.Rd
715674e5726e9984e1f4a0dceffd0f94 *man/SetAssayData.Rd
1029e6a8f77a5bec3f1272a5b6c8579c *man/SetIntegrationData.Rd
749dfea6bc4fd4f973cc03ffda8d1327 *man/Seurat-class.Rd
5bc491ce76fc423e2e566fd61aecfaa6 *man/Seurat-package.Rd
a5840df42a5320da92ccc80c8e0a2c70 *man/SeuratCommand-class.Rd
39b2c325e1c1497a43b2ae3e24ff0316 *man/SeuratTheme.Rd
3e01377d95816ef7296b93205f934bad *man/SplitObject.Rd
10b4efde5824a0eb4a845660b82728f1 *man/Stdev.Rd
0b56a6fe26123ba2c87ca93ca0a3d12e *man/StopCellbrowser.Rd
795c05a5f6b0d4330dc4245749aa87b0 *man/SubsetByBarcodeInflections.Rd
23a1e88f6742bef1b652cafe03457419 *man/SubsetData.Rd
3cf18a0619327727b30e4eca0fbbf98d *man/TF.IDF.Rd
79b32637ea153b3f68bfc99e5144e7e7 *man/Tool.Rd
baadd91d4ee8241049cd91da75fdb979 *man/TopCells.Rd
0fc6ec673378c4292bd76c81456e639d *man/TopFeatures.Rd
8b011ae8da7c06d2863b887d225af148 *man/TransferData.Rd
a6dd88aeb59cc35bc0c499faef6f8245 *man/UpdateSeuratObject.Rd
25a7efa512f64600f0d03ff07bda3c47 *man/UpdateSymbolList.Rd
7f5ffdeb0f719df359d9a1386272506b *man/VariableFeaturePlot.Rd
94c64679fb550f6e317073f5d70106ee *man/VariableFeatures.Rd
d0be07370d2e7c61688d924f17a37fed *man/VizDimLoadings.Rd
02fa557ea4fee43dc193ca15097e185c *man/VlnPlot.Rd
dece0d5191be191520e35efad014ae44 *man/WhichCells.Rd
7ee1c557a525878f1fa578050c020573 *man/as.CellDataSet.Rd
186e2c44f694fe115062f3e4058c509a *man/as.Graph.Rd
75df80df56a52cf1f7a91c5a548f8001 *man/as.Seurat.Rd
dc04bab144868edf9e3011883f9b34df *man/as.SingleCellExperiment.Rd
29fa8aad68535bd377eb6ec5cf4489b4 *man/as.list.SeuratCommand.Rd
358c060401fb78bf20f609db43c63e35 *man/as.loom.Rd
7f89cc204da9d903a8e41fcfb20fc7f8 *man/as.sparse.Rd
7ffe0ae1501d78c342893f8a859206fb *man/cc.genes.Rd
0a4be74c783011a9247694c1185647b4 *man/cc.genes.updated.2019.Rd
b24f1e27d63f78d4597211eeccb8a875 *man/h5ad.Rd
05b14093f43330f7a9c5604b700c7a30 *man/merge.Seurat.Rd
c83eba96209207d78ce66966a6d92d8e *man/oldseurat-class.Rd
8d538b155ece42aea42a541c4de3c65f *man/pbmc_small.Rd
4a836c72c3c8fc443ff7cb6f6fd47cdc *man/print.DimReduc.Rd
12dc644b63c647937cf495098feee42a *man/subset.Seurat.Rd
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
2d00bfb3d70dd902867ef8b93b77ac43 *src/ModularityOptimizer.cpp
fa50cfd47c172ecdbb147c0958a068a4 *src/ModularityOptimizer.h
6b14b655eade640931673c1cc1357a6c *src/RModularityOptimizer.cpp
91663f44f8381d76fc119e6a8c5d842b *src/RcppExports.cpp
55a7c5f0d560a759aadbc621952d2f60 *src/data_manipulation.cpp
33c323c457423699649a725513449e14 *src/data_manipulation.h
efdafe6d860a47a3c5ed9642846eb009 *src/integration.cpp
d03bd7b8e78939ba29e8f31697e3fc48 *src/integration.h
fa46a78e09a6479196ef7a4bcc0ee0b9 *src/snn.cpp
694a8ab034ccab2c5f7c35bf47b3469e *src/snn.h
1d5009992bb3e703bb3f2482f9b8ddd2 *tests/testdata/barcodes.tsv
d2554fb8e4d5af543605d0a729e36109 *tests/testdata/cr3.0/barcodes.tsv.gz
70e1ed4c347e2563a90fd2144f375a26 *tests/testdata/cr3.0/features.tsv.gz
75dc5f8ba97f4c3bc30ceb7926c5759b *tests/testdata/cr3.0/matrix.mtx.gz
91aa47aeda59ef6d82105100a09d1497 *tests/testdata/genes.tsv
6693f4ae1a15e0985ed513ee83fad927 *tests/testdata/matrix.mtx
646ac9cb85813dbe838d804f78f717a4 *tests/testdata/nbt_small.Rdata
34b405818933dc96aac3fcd6594b483b *tests/testthat.R
941318016d93b998980beadf040d4170 *tests/testthat/test_data_manipulation.R
723ee1d34ca4174358fb8fffb1236139 *tests/testthat/test_differential_expression.R
cb6d9cbe4ed7f0154b6fa345f0273841 *tests/testthat/test_dimensional_reduction.R
84a1a4b716c9f780c4daef3357fcec73 *tests/testthat/test_load_10X.R
e096ae1c8e0ea82b43c0e5ff4c5ba116 *tests/testthat/test_modularity_optimizer.R
1031adb903cd86443445b33f0d7a4954 *tests/testthat/test_objects.R
3b9df16a82ab38d9af0d31f212422c76 *tests/testthat/test_preprocessing.R
fe4445fb9c845a7d9163022b38112548 *tests/testthat/test_visualization.R
