e5c78f7263e62e5bfad209e244502fb5 *DESCRIPTION
4e3059b3db4e1abda3a89b088a962f47 *NAMESPACE
765b5622f97f608108ae4c53e4cf82c3 *NEWS.md
e1a6e77d814d7432ef499d85857032f3 *R/ATAC.R
b977f2b49f46f91412100976c2759286 *R/DEG_marker.R
263c4a101fabda184ae09e183df52937 *R/DoubletFinder.R
ca78128e52a629ffd29cbe565ef96681 *R/GSEA.R
5b5ad09148a2fb0f9b43d7fa02d4c221 *R/RcppExports.R
db9420d196ad9bee62b92352fb9d9430 *R/aaa.R
c577269e89a430d38cdcb43d3e9d0132 *R/archive.R
c1bb71f79b636806afe89d537c666ed6 *R/cINMF.R
1c317cd6241a734c8e341d2550bab9ad *R/classConversion.R
bd9a9911e52486381ec3a0cec7a88038 *R/classes.R
f6f9c94ac5f6324f6255c148356eee87 *R/clustering.R
7a7088c0c2f41dc2b5e2bd50b1b21218 *R/data.R
7a7a84a61e93dc6346c5dc37ac5bc568 *R/deprecated.R
0a12bec1b58f9b036910c4bdb641d4be *R/dotplot.R
b4c3f4ec502264c348b62f4b3089f222 *R/downsample.R
8d593f638ef729ca69b7e1cee2f66735 *R/embedding.R
bb40c7b840e9bcdefbc429f8f50cfcb2 *R/factorMarker.R
d3d8db03616af793c10040a4ec962e83 *R/generics.R
fa122792768ab7a01b1235fa505d44d0 *R/ggplotting.R
df5e15c9ec2828c65d7b76d84b0f0505 *R/h5Utility.R
1aa6d7de9d01b302035d85611c066529 *R/heatmap.R
b837517c1c62a68109e5bd22c9960eea *R/import.R
061303c4d6f865e25dedb3cb8de2272f *R/integration.R
a4de26df81c5643511a03b05da2c0ba3 *R/liger-methods.R
868c006ce690402f4977652454cdec10 *R/ligerCommand_relates.R
0c0ee418ea9c5ca84dd9ee8e38117147 *R/ligerDataset-methods.R
596126930649f6ee92092f0c0f83860b *R/ligerDataset_subclass-methods.R
d10614b5645a27c868a5edb6e98db70d *R/mergeObject.R
8a2879a5b55fa45c631f194ff18a4e81 *R/optimizeNewParam.R
fafe5619cb106fdd9091cf3df7b04488 *R/preprocess.R
c79535335fcc45b4a1def7e065eafaa3 *R/subsetObject.R
3d00e3216b3faae93903174e733a7265 *R/util.R
66b8793b276d66e072caed56537b2797 *R/visualization.R
eaf10adb74ed275d6320a7db80911b58 *README.md
41e6020ce9742606a360f57289d541a6 *build/vignette.rds
5cae1eab838da773bfcf6c76cbcf099d *data/bmmc.rda
96d5bf04243314c34c8688cb9e56deac *data/pbmc.rda
f7e24943e840a5d1957d37f38adac05f *data/pbmcPlot.rda
0f642a5e13a602254d44e845af19fa1b *inst/doc/liger-vignette.R
2dcb5e1a0f5c1ed12cb1c7228b859072 *inst/doc/liger-vignette.Rmd
91a97e1f3e9e8a0913d719e08cf2da58 *inst/doc/liger-vignette.html
c65470d23298b60ac70c6a5b867fea9b *inst/extdata/ctrl.h5
ecf84fecd0da62b735655e281d0492e0 *inst/extdata/hg19_genes.bed
a5f1b28304910d164707213e31054675 *inst/extdata/stim.h5
8fdda9c4422d30ea3854bf22f5bf6b8b *man/H5Apply.Rd
8d8c9d7c6d1324ba480a25f25c3318e8 *man/as.liger.Rd
82658feb51771663047ed3b27d6fad91 *man/as.ligerDataset.Rd
9bb0848b925d4afe1b38e40706785efc *man/bmmc.Rd
621aed1a9b6452413478b53136054516 *man/calcARI.Rd
072f15f59203128a2fbd939ea8c89dbb *man/calcAgreement.Rd
1a8d998edebb796702b03e02dc69a9a5 *man/calcAlignment.Rd
c2e806e200bd77207dd64be1f1047bdd *man/calcDatasetSpecificity.Rd
6c074f6c9622b51d9158a2686b88384a *man/calcPurity.Rd
e567289eb8ba1178658d22b8fdc640dd *man/closeAllH5.Rd
8998ab62a8fa73414e97459463e60983 *man/commandDiff.Rd
1cf03955bf149514ec940613441a347c *man/convertOldLiger.Rd
63264137d2bd2df7410ec79a2d4625dd *man/coordinate.Rd
301d5509dfba30bf8e4d6bf4ed7cf9b0 *man/createH5LigerDataset.Rd
0825ee79b8f5f29173e81b8c26e53d8c *man/createLiger.Rd
d87fd9aa465945819d02093baaf2779b *man/createLigerDataset.Rd
245f090638b99624a2cf4c29777bccfc *man/dot-complexHeatmapDotPlot.Rd
e71781c68697929c0015b9c330c187e6 *man/dot-ggCellViolin.Rd
c377bf746e2cc3f3e88f18365871ab4e *man/dot-ggScatter.Rd
0350f8936c6a12303a79faa6c95f55a3 *man/dot-ggplotLigerTheme.Rd
0f92e230170c81ad77214c931ee6bb08 *man/dot-plotHeatmap.Rd
6ff6989e3abe4fa61245550c54f79ae8 *man/downsample.Rd
ec312ee2cbd4a4fccc162f37169d54a6 *man/exportInteractTrack.Rd
52c344bf2b2225e634bd91420dee7b93 *man/getFactorMarkers.Rd
6aba44ce2cf18d1c3a31836a83ceb30a *man/getProportionMito.Rd
a28f3e6bab1631a0c79caac644ce2440 *man/importVignetteData.Rd
e1d44800ed82863e4eefda892141cb5d *man/imputeKNN.Rd
d06f3de7c9d9d07790d9391bd1000d07 *man/is.newLiger.Rd
7a83dd94560b3ecb9fea2bd1ca453059 *man/isH5Liger.Rd
83cac291af9dd68e63138e3aca8804cf *man/liger-DEG.Rd
731e5cf660e529f21863256c39a6ca80 *man/liger-class.Rd
3439cd2c5a7c4213018e1d1342352476 *man/ligerATACDataset-class.Rd
f769b9e11b413c42d7cdbd6a2c92ed3a *man/ligerCommand-class.Rd
b0e91da2d2a20cee17887643aa96a926 *man/ligerDataset-class.Rd
d1c35ea11d20ffdf819f59e516a97abb *man/ligerMethDataset-class.Rd
0f018da2257e4af5f5c00f900d20ed32 *man/ligerRNADataset-class.Rd
5c1b116b853e847fb1b34280a6d92f13 *man/ligerSpatialDataset-class.Rd
2f8a798f147a0121b9460d0e2c6838a2 *man/ligerToSeurat.Rd
0dcf3990f6e4d182edd855019392335e *man/linkGenesAndPeaks.Rd
1fb1ec856149e331cfe780365369921a *man/louvainCluster-deprecated.Rd
d92afcec885b6810069cd32b9dcc7ec6 *man/makeFeatureMatrix.Rd
ddbba9cc5e3115851ffcb9d79c9c4d0d *man/makeInteractTrack-deprecated.Rd
ce3bada4c1d71d18af1a4cdcd6125547 *man/makeRiverplot-deprecated.Rd
84cceb1b9900b335d4bfaa43b56bf91b *man/mapCellMeta.Rd
b3d72496534ce837113d5c49b039f713 *man/mergeH5.Rd
03d4bb9962c0cfb69a5c37224fc59e70 *man/mergeSparseAll.Rd
0f449bba336bea645d8288ac517e944a *man/modalOf.Rd
3a710b11f1c017edcad736d2553b658b *man/normalize.Rd
808f390a119b86f46cd98433dcfb1048 *man/online_iNMF-deprecated.Rd
73173ff1deb1d8833f8ad5ef9b189d03 *man/optimizeALS-deprecated.Rd
438b4f89c05ad42d553f235de3637fd9 *man/optimizeNewData.Rd
a1b0eefd02ec5db8b2e32ea7edefccef *man/optimizeNewK.Rd
c27a223208d5705b8e925ae99213115f *man/optimizeNewLambda.Rd
5f6c83ec737a1923ecbd26e5df7fea4b *man/optimizeSubset.Rd
8073b085531b1fbffc963bae6d93d821 *man/pbmc.Rd
89f0e14e713b021308c84cbfff276e7d *man/pbmcPlot.Rd
eec71b3de35642eb45afd8bf26fd764f *man/peak.Rd
c052497d64d252082162c7c7955527d2 *man/plotCellViolin.Rd
f33d8acdbb1bfc1e6b4e5df4882f4f69 *man/plotClusterFactorDot.Rd
55bfbc4a292807662c6337d86ecf290e *man/plotClusterGeneDot.Rd
97245dee6dd4e81050c778c05a39ca8f *man/plotDensityDimRed.Rd
250b46a3b283844bf19b738984508f98 *man/plotDimRed.Rd
604500529c8d9302a752fd154f767031 *man/plotGeneLoadings.Rd
2848ff699bb389bbd14435df1dab26c0 *man/plotGroupClusterDimRed.Rd
1b5721e925db2a96797040066e953f18 *man/plotHeatmap.Rd
db5c08ee92570229565f631ca29a26f7 *man/plotMarkerHeatmap.Rd
6d85c6f4a8ce092494cb3075eb1acedd *man/plotProportion.Rd
43c866d723261aaaaf598523565df7f9 *man/plotSankey.Rd
6c0feaae69fe25fa8c6b9917cbc1b04f *man/plotSpatial.Rd
600f9d3d9f82e46a6dd6bcca3732aaf8 *man/plotVarFeatures.Rd
7965ffd9d0764288bfafe47525bc684d *man/plotViolin.Rd
ae8b4e830278a8ca8744984e9e35fb51 *man/plotVolcano.Rd
b841a6bed5bd1a074cecf8031041b34c *man/quantileAlignSNF.Rd
c919820478586cc500772da1a53492b8 *man/quantileNorm.Rd
0f166a1f8fac020f80f1161c755646c0 *man/quantile_norm-deprecated.Rd
7b9194af695a80f74bf9ee8b95cf7026 *man/read10X.Rd
ee5cdd8c64f07eca34cb4a2f6e247042 *man/readLiger.Rd
25e603fe81c971068f95603b1dca2f1d *man/readSubset.Rd
6a483e25e17060e1d6db466d2ed75695 *man/reexports.Rd
b23dd944def81ba71a72f64e2ccc7fa9 *man/removeMissing.Rd
b5c422841cc9c7d70972354e21c91481 *man/restoreH5Liger.Rd
c8cb13cf9ca1027a9bb5bf3695cf8897 *man/retrieveCellFeature.Rd
9631988cd33f7a87fa0e6815bcf1bba0 *man/reverseMethData.Rd
323a81f105acb986b81fb3f987c94e22 *man/rliger-deprecated.Rd
f826799e3e97b9137a34959ed175a4e0 *man/runCINMF.Rd
bf5d2ef83d6181573caa29e1a45554e7 *man/runCluster.Rd
e0d5cdf568b749140f28f8496b640ef3 *man/runDoubletFinder.Rd
1e573d4874d666ebfd1a218506f0d2b6 *man/runGOEnrich.Rd
1f1ba80d161c3ccacbecf0309928fadc *man/runGSEA.Rd
f69747836d9c2ced1c03792536e078ac *man/runGeneralQC.Rd
8fd106916afe8683d136168aa9ffe6ae *man/runINMF.Rd
9aac6aab4c9eaa19f308bbd388f09b87 *man/runIntegration.Rd
3226f45070554e37d50cce1f78524d87 *man/runOnlineINMF.Rd
d370433924c15440b69555053b77a9c6 *man/runTSNE.Rd
bc7bba2207f200ee65a3472cdc2b4b48 *man/runUINMF.Rd
4936b0679b2c63a2c26203be2db80253 *man/runUMAP.Rd
e529ca9296ef01070344d295fc7f026f *man/scaleNotCenter.Rd
af7d7075ed4614f2d70e5f443de606f2 *man/selectGenes.Rd
b71cd3dbcea6b491ab1706425e3b9ce0 *man/selectGenesVST.Rd
b571728a6ec4e46843d0f626d46991ab *man/sub-liger.Rd
b2f67b2047f805e709cd9aea2d1ee73a *man/sub-ligerDataset.Rd
8ee738b64fd951c244eaa8675acf31c1 *man/sub-sub-liger.Rd
4d54a4703c8ab522995c19adc7054038 *man/subsetLiger.Rd
00f33b8eff5f0bdf6d3157ef54e19e3a *man/subsetLigerDataset.Rd
54c534ec36048908fd537ff2d228f6f0 *man/writeH5.Rd
29bfdfcced57d846e658fcb684c0261c *src/Makevars
29bfdfcced57d846e658fcb684c0261c *src/Makevars.win
7e5cf32d81c12a5362b3739355d94802 *src/ModularityOptimizer.cpp
0bfda1b8f1b6d7667f7ef534168b8c8a *src/ModularityOptimizer.h
c1fb199b6a902f4233bc918b6335a8f5 *src/RModularityOptimizer.cpp
f452de382bb2d52fee04201162ce412f *src/RcppExports.cpp
f820b1549535d4c309edb49eaa79e478 *src/cinmf_util.cpp
cd410cbec47008814d7c595a834765ed *src/data_processing.cpp
2095efd213ca2c8fbaddf18531690846 *src/feature_mat.cpp
598152f482b05934286a03752cb56de2 *src/quantile_norm.cpp
fff3def2df358ef7d5f6e32db658eb2b *src/snn.cpp
a28e8648b25d2e780861d74a015e6b32 *src/wilcoxon.cpp
ded24bd60a18e5bbbb6dabea7b75de00 *tests/testthat.R
6e277d49fa221180f030492df7da2861 *tests/testthat/test_downstream.R
0429d529d6a12f01b2331f2de7161a0b *tests/testthat/test_factorization.R
26ad307ff93659f6400830ac6d0cf259 *tests/testthat/test_object.R
970b821815f246321f7563cae3764ca0 *tests/testthat/test_preprocessing.R
ce770ed472038f0c0f3c95dab55d12ed *tests/testthat/test_subset.R
ddc1b8e0311be9aabbb703e44087e13f *tests/testthat/test_visualization.R
2dcb5e1a0f5c1ed12cb1c7228b859072 *vignettes/liger-vignette.Rmd
