d6fdec8cc70235b40086d2cea93b02a1 *DESCRIPTION
7d429226b4b6e0d6471ddf9cc520e3e4 *NAMESPACE
b8e3729a5777fb56c495e54dd7301a54 *NEWS.md
cec47d3bc8c41f1e67e8910ec6e11b07 *R/RcppExports.R
2e18126fc566ef82227c48dc05923f51 *R/data.R
1a684befd6ec9fef45c8b99694344521 *R/deprecated.R
76756bce5d0a5e32029246e3723766a3 *R/rliger.R
57d05a596652878e764a8a1e41d2d1ba *R/utilities.R
77546a7196a9b89be4ed5f1b749f2387 *README.md
0d090bb10f52886deb176d80fc44d169 *build/vignette.rds
aba28d10bff5fd7117b0efb70e0beb9c *data/ctrl.rda
3bea953e3ffcf8c52d95d2e3a65c09ac *data/stim.rda
46750e778a5cdb4d65c347f8e43df623 *inst/doc/liger-vignette.R
6c57385e0da6424e7f7dff98be4603ff *inst/doc/liger-vignette.Rmd
2b2f4b7f66848474597a38e612c29479 *inst/doc/liger-vignette.html
9bc153f1ac120e45fbd86143e330858c *inst/include/rliger.h
e35e84bcd236c5ca1fc6c45596da109a *man/calcARI.Rd
b59a5c47c2eb4900e684f4383808bb77 *man/calcAgreement.Rd
f3479373536f67e663ac5dc5f9ea9c14 *man/calcAlignment.Rd
1677a5974f0d2973bbc649e2d2614176 *man/calcAlignmentPerCluster.Rd
09f32536c48e68b82ff07f2a2a96b3a1 *man/calcDatasetSpecificity.Rd
34a7802a5039cd04454cf029c050763e *man/calcGeneVars.Rd
526ee4e4e6aa4efa66149bd5026eead3 *man/calcNormLoadings.Rd
f10eddbd3fe5d9fa8b40945c9378582e *man/calcPurity.Rd
e78437c4b3f0de817251ce677bd9e2d7 *man/convertOldLiger.Rd
e7a979ee06f8b6e3ec5619c8dd39c0fc *man/createLiger.Rd
1f6721993948e5709a0502a9ad16f548 *man/getFactorMarkers.Rd
abbcbfed2049711c389293ed2edba29b *man/getGeneValues.Rd
173cb62983f79d4733a30d68bf549459 *man/getProportionMito.Rd
ef7a0a30a92dd869b6003c0751b1dd81 *man/imputeKNN.Rd
cd10793b564ee4836509f848eb095572 *man/liger-class.Rd
064658a2e592cce5ea69cdb3f54f9b99 *man/liger-demodata.Rd
4a8090a7ceb8e8b27049e83e7d84fad4 *man/ligerToSeurat.Rd
f3768be971cd45ebc5753c04eedeba56 *man/linkGenesAndPeaks.Rd
93781489b20ce789949f2a43973dbcf7 *man/louvainCluster.Rd
d92afcec885b6810069cd32b9dcc7ec6 *man/makeFeatureMatrix.Rd
d3a96ab9ce309049421c90e9e5bbe50c *man/makeInteractTrack.Rd
a117a3654f16fd1fc6037a4c9358b681 *man/makeRiverplot.Rd
374a69a53fd5acb903bfad5b05b7d752 *man/mergeH5.Rd
665974e5c37006ac3be8049d33c67301 *man/normalize.Rd
70418e5f34f09bb1f83769e574c428ac *man/online_iNMF.Rd
0ceaaba05934e160899ba3890cd78289 *man/optimizeALS.Rd
49c1aa215b93e59d022ce5a161d723ba *man/optimizeNewData.Rd
2d80aba5e8374af5b941b0ff7a889415 *man/optimizeNewK.Rd
a6b261342993016dee77e5c803afab0a *man/optimizeNewLambda.Rd
61d3b32652ff75156e31b8ecce85cbf4 *man/optimizeSubset.Rd
2bf3c3f23bdae8baa3b11cb5ddfc2982 *man/plotByDatasetAndCluster.Rd
7952c5551e23cea69ab01d26f6ee22ca *man/plotClusterFactors.Rd
63e6581c99735121c7ee381fd2d50b4f *man/plotClusterProportions.Rd
ba3451375c2945a54568920dd2906558 *man/plotFactors.Rd
7e10b2c3b97a176d9b166e9591f0a2bb *man/plotFeature.Rd
a2c803b2e8e74ba8c9c512fcf199e454 *man/plotGene.Rd
9bc6686f5cecca4e88fec7cd43d7d5ff *man/plotGeneLoadings.Rd
6f4426636f04323ffcf70cdf848707b1 *man/plotGeneViolin.Rd
a860642cdd489804cfad13be88b1fd28 *man/plotGenes.Rd
61146aa99514687ee934c869d3e0553c *man/plotWordClouds.Rd
ec29a4bcc029526ce0b51ebd084c621d *man/quantileAlignSNF.Rd
9e42acf8b099466e80f2b0c912a9a094 *man/quantile_norm.Rd
7639c638bc16c103e7dc4cdacf270724 *man/read10X.Rd
dd096cea6d56c2967d9a25c5f3b7664b *man/readSubset.Rd
1e2404142e89230c74248c8c3e1f9703 *man/removeMissingObs.Rd
045d636d5becf021e17cb21848d64a91 *man/reorganizeLiger.Rd
3116381431a0d32e3888c1d19d0db21d *man/restoreOnlineLiger.Rd
ae8eb8885b6b9686d0d233d25886abde *man/runGSEA.Rd
e01053144082eeef6391455262993497 *man/runTSNE.Rd
486b93893ed690917e8e94078311197a *man/runUMAP.Rd
a6a120c90da01b43a00d69575e521f1d *man/runWilcoxon.Rd
8331f1bb42d6f694567100568fb5dcc0 *man/scaleNotCenter.Rd
a0d0c6e5565a71206c971c8b6cd64cdc *man/selectGenes.Rd
c8aea661785b87f97e7a3f72c2897f1e *man/seuratToLiger.Rd
181098374b15976c46524b0d4f45994e *man/show-methods.Rd
ec648fbcb03879f74401478a4577a214 *man/subsetLiger.Rd
be62b01d9aa4985c0eb4144dc6b7a97d *man/suggestK.Rd
fa55d9bd6780155934f3a939102fcea9 *man/suggestLambda.Rd
896326ed4956c56d17acd540bb7f0107 *src/Makevars
ea7836e0289240cdfb3ffc7b9fc60250 *src/Makevars.win
3e7bc8d512b37a4fbb15aaa05349767f *src/ModularityOptimizer.cpp
4478d72a3694be06ff32fa303ba13852 *src/ModularityOptimizer.h
262eb673da9302200241deb67e40500e *src/RModularityOptimizer.cpp
5b0ae05435b0c4887898b90725720755 *src/RcppExports.cpp
1e6898c4ba40b1b4e4651d2bb84ce97a *src/data_processing.cpp
9d735dd495bcf7d619b9424325761b40 *src/entities.h
e4d0ab15b0365552fef969c6d4618288 *src/factorization.h
b6f2da687410b46ca45208c9c992f84b *src/fast_wilcox.cpp
a4ad1f9f30cd9303db7d975f10b453a7 *src/feature_mat.cpp
6b932c3e332f876c3da77d53ee095a57 *src/ls.h
dbb5043a12e19c683ebe3ee711836177 *src/mask.h
20ccf9b2a39e4f1eb70b2983995c0b17 *src/matrix.h
ef7b379226b0b1fcc9e65c2408a2e157 *src/nnls.h
077f8122b06ee572933820b9ec9140ce *src/parameters.h
a19b1e6f6a817842c5ca049dd8595155 *src/quantile_norm.cpp
b9762564c79083c41b3f23cba30d39bb *src/run_nmf.cpp
880f8476171cc21ed390beee82e548aa *src/snn.cpp
8bf60682ebafd2bf4bdf94d7640fb7a4 *src/vector.h
c84fb7cdafa84346cbf72b2f4d2be2e3 *tests/testdata/small_pbmc_data.RDS
ded24bd60a18e5bbbb6dabea7b75de00 *tests/testthat.R
b5b85e6f05e3bd0ed9960bd8f1bc350e *tests/testthat/test_post_factorization.R
9ce41ce666b64ca8e8570f86237c6443 *tests/testthat/test_preprocessing.R
6c57385e0da6424e7f7dff98be4603ff *vignettes/liger-vignette.Rmd
