88621c71aa68d50357c632b0f4f18634 *COPYING
d53207bfcc4a5ac8316a33074616ee42 *DESCRIPTION
ca4ad319a216c6ce155dba7226fac52e *NAMESPACE
cb29408f24ea43b8c7786557906af7ae *R/PMmmgmos.R
04c4bc6a2d32dc01ffc578f804b09a36 *R/bcomb.R
c347536392f6a5bcde912271db7d76d2 *R/calculateLimma.R
0bd4aa46fb196f568fd2cf6b8091cbd3 *R/classes.R
163432e13e134c13abd19aab07ff1386 *R/compareLimmapumaDE.R
ed1478758120dfd62a7325eb99fb8391 *R/create_eset_r.R
dad06fc4b28e47c2eda5febe66342d40 *R/esetFunctions.R
721e090986ba73c6f1cd4081f3bbc2e5 *R/gmhta.R
95c5d683f81b87316fe81b960378c696 *R/gmoExon.R
5dc9d54a9f9d22ab74102cf5c125c595 *R/hcomb.R
de7e1e181ff7e7e518924e6e113430a5 *R/igmoExon.R
d69ab53663593ead1888b429116483c6 *R/justmgmos.R
ce15192560aa48980d5881b8fd57af2f *R/justmmgmos.R
0be2313ebbec5b9f723f6f5fd8e0db9d *R/matrixDistance.R
ce4ead475f7f683dd71fbe41c5f5fcab *R/mgmos.R
65e33801c9ece3040acc14251ce6bb77 *R/mmgmos.R
8db50a244889d721097a93c1ba83caad *R/numFP.R
e103ca13b8738a6d1aea9e005fa6d262 *R/orig_pplr.R
ae85b99a70d466f1cbd2eb217c24957b *R/plotErrorBars.R
d80f74cdc179edff27eb3260e8b7c434 *R/pplr.R
de1e08f45ca64dcba4dfb0e6e354a8d6 *R/pumaClust.R
6ff3fa892eb24232df392c4e1dfb905d *R/pumaClustii.R
b15ed69410510877d21614655beca79c *R/pumaComb.R
0ed6d41cdabb0e98e1fd718cc525b514 *R/pumaCombImproved.R
4a19f8f81bf7d6ac26d38c7c5b9d79b4 *R/pumaDE.R
6e16b838eb593e1619f20227d6b5173e *R/pumaFull.R
9e2dd727c27410fe26f9b4090fa30fe5 *R/pumaPCA.R
d308f99f228d109fc8911f6bcb5af4bd *R/pumaPCAEstep.R
a6d8fc82759be3551300d47a5173e66c *R/pumaPCALikelihoodBound.R
9efc49c28e7e709cd72f57a6910ca92e *R/pumaPCALikelihoodCheck.R
ff535c3f89828a9e09d33f933f75fa64 *R/pumaPCANewtonUpdateLogSigma.R
4822a6cf0f550c7ac233c34dd19be7ac *R/pumaPCARemoveRedundancy.R
d58ee95cb791de39cb439b0b907dea83 *R/pumaPCASigmaGradient.R
e366d860c61cf2c7db9ff32fe66d2f13 *R/pumaPCASigmaObjective.R
91441668ef2c9282f36980efa1fa736b *R/pumaPCAUpdateCinv.R
108cab81a75cd26de99c390262a57dfb *R/pumaPCAUpdateM.R
4502c90ddfe081d70130f9c21815bfa7 *R/pumaPCAUpdateMu.R
fbcc0a5e1d13beaa8393135e20ab5ce3 *R/pumaPCAUpdateW.R
26ff60003aecf8ecdd897cf36ed82b5e *R/pumaPlots.R
e861d791e4c0a008098a4e928067eda7 *R/zzz.R
d6544cc023c0b002726fb7716bb7f536 *build/vignette.rds
7189dd3e2a837fe278763335e5585968 *data/Clust.exampleE.RData
e02ac8eb33472385f7e2493c63f13e40 *data/Clust.exampleStd.RData
3f1369e511f140871e1d4deeb456d8a5 *data/Clustii.exampleE.RData
8485ac65d4d5ec549b05ba0e327aa114 *data/Clustii.exampleStd.RData
76eb8e6aeb99e96788a209268c39b21f *data/datalist
5cb979f1fb0dde9e93055d63cebaec85 *data/eset_mmgmos.rda
f73171722b42ac4f7ac15725d1a7da27 *data/exampleE.rda
c926d4729bd9fa413509c746dc701a61 *data/exampleStd.rda
2245175ff056fd1951eec5a83183001e *data/hgu95aphis.rda
6c6d556705e80cbcb80e1a73db97ce1c *demo/00Index
2ab7990c2836e03541e8ee246cf34575 *demo/puma.tour.R
b4b707c965db686e07d62b11fabab52c *inst/CITATION
4614b9470c968a9a7894b196eced7b85 *inst/doc/puma.R
065461b57d8e7705c9c2431314a175f1 *inst/doc/puma.Rnw
809663155f7df2d5dd98daf08bad7275 *inst/doc/puma.pdf
ea9890a77eb60d0a45e09d00eaf5cb28 *man/Clust.exampleE.Rd
8ce5ada9643dae0b2b274a3d959d2388 *man/Clust.exampleStd.Rd
9d405966e773140c68a8400b69ac494a *man/Clustii.exampleE.Rd
b8924404cf07d98806850a08a234a675 *man/Clustii.exampleStd.Rd
7e9542b82896993f5976b706531c1bad *man/DEResult-class.Rd
bfe86a810333f64fa836a53c585c46e4 *man/PMmmgmos.Rd
fd70ca84a9f07bd765320e4d5c469b10 *man/bcomb.Rd
4fb968a97718709e8834dd2c35a3cd02 *man/calcAUC.Rd
c47ae64090418bd355009cc04d36a11b *man/calculateFC.Rd
f7dad5bcce3caa182e9a31e16c663734 *man/calculateLimma.Rd
1728478b989af8f38d414bcf36443e55 *man/calculateTtest.Rd
f53ee543a9355db639b1392897e548d5 *man/clusterApplyLBDots.Rd
1308aba5d574b4ab82da6db1ba7d2088 *man/clusterNormE.Rd
d204f787e6784f7816ea92a29e62e050 *man/clusterNormVar.Rd
dcf76f328f662fe3d52180a3a314e3aa *man/compareLimmapumaDE.Rd
3e53f74ba8d4a1f6a91d4f1b3ef209cb *man/createContrastMatrix.Rd
c43ae937022cefd49b82a5495741e4cd *man/createDesignMatrix.Rd
c55b965b3c317768b43554f6f7c74571 *man/create_eset_r.Rd
6a039a4dd0bd09e01ed6c73ce2d72ff2 *man/erfc.Rd
0b0d7e6c96fb43853c6792b3619f1190 *man/eset_mmgmos.Rd
cf106dbbd0d42a415a2db75d860462c7 *man/exampleE.Rd
58d21d5a9c4f3b3a12b7c9378ec33e19 *man/exampleStd.Rd
55ae1dcb82a092c01dfac4e4d048be37 *man/exprReslt-class.Rd
eeaae46dbedf07650a83aca989dee430 *man/gmhta.Rd
48d1dee0b6d8f14c7a10ed78fd94992e *man/gmoExon.Rd
d1d1c1119eba51f59d3b350f69bc01c5 *man/hcomb.Rd
cd2bbfe53d6c77fd2c8faf89d22f1191 *man/hgu95aphis.Rd
faa15b9583767f4d61c2954298ed5a24 *man/igmoExon.Rd
1cb774aef452a8dce02c9840bb456112 *man/justmgMOS.Rd
f164054f32c60475223a7acfd8af560a *man/justmmgMOS.Rd
cb516452384b5f6c9903a01a55679000 *man/legend2.Rd
b97b8af7117f2b361d1c5717fe171e89 *man/license.puma.Rd
a38036f1b4d09d1b20303c95d0ba603b *man/matrixDistance.Rd
12e55f6cd8f5d6a2cc2e92232080dd2c *man/mgmos.Rd
0c2f436a785d3b1683e18bea2edfbfbb *man/mmgmos.Rd
b025278a9bb8c77601bc52bcf236702b *man/normalisation.gs.Rd
49d5d76bb4c1fcbc8fe32e98c58c23e5 *man/numFP.Rd
5cd8004183622b283766c5af9bfe978e *man/numOfFactorsToUse.Rd
b0fd090709733f1e46dc505599deddc0 *man/numTP.Rd
88fd0052ec3b5fa3e67b81db5affdf8e *man/orig_pplr.Rd
2154c12554c4a599d1612ca8cb67eb4d *man/plot-methods.Rd
a21ba2ef2918350ef0afe2bc004d8dc8 *man/plotErrorBars.Rd
150bd30a6da2e2ee85fe1fc7656b100d *man/plotHistTwoClasses.Rd
1aebb8e662d6bec7179f9fd4e360916c *man/plotROC.Rd
2f0111a7bdb12a59b569937e5f49dabb *man/plotWhiskers.Rd
54258861fac9f4a69ce07b3a00a64ecc *man/pplr.Rd
a208c490947477ce588b28c42f5ad7f1 *man/pplrUnsorted.Rd
655f9ba47fb550c02c32e9645f94d9bc *man/puma-package.Rd
8e0df4f5e1d46ca20cd66b7f40b94296 *man/pumaClustii.Rd
6dc2c9d49804b1231336961512805ebf *man/pumaComb.Rd
1f6271304b9352383b909f70210cf320 *man/pumaCombImproved.Rd
b4160b4c63ac4bd5b2318bd6399eda0f *man/pumaDE.Rd
c6987cf642c09c45b37261bb4951cb97 *man/pumaDEUnsorted.Rd
e37c2cf28446a5573f94780e5b4cde5e *man/pumaFull.Rd
b02c5e0484d1fce87562ce979fe14c71 *man/pumaNormalize.Rd
e1393d1a9b5b58e2208fcbb9627fb747 *man/pumaPCA.Rd
c4ec89e9a33fa1944ee1605d0deaf804 *man/pumaPCAExpectations-class.Rd
45dbac6b51ba3a36fa80e1459dab8e7a *man/pumaPCAModel-class.Rd
feaf91fa6080d06b37472c472c99a4d4 *man/pumaPCARes-class.Rd
bb8cfef1832ce90714d7eaeca9fc5569 *man/pumaclust.Rd
b8a47f70c01d996dd4aa87508f31de47 *man/removeUninformativeFactors.Rd
6f9e25e194f38bb62f78321034e189d6 *src/PMmultimgmos.c
10ce0d60aa09612dddd898924eeb65eb *src/PMmultimgmoshead.h
795430097b47ab71bf5f5c4e222385e9 *src/cregistration.c
3fac5b270631198900ced52aa4742e9e *src/donlp2.c
2ba35e87151182b1f603f7f86c15b0a7 *src/global_constants.h
c0cf6cc651bc5902b22dcc9b4d71b99f *src/gme.c
bfd0fbd7346d07743f2178bbd4283da7 *src/gmehead.h
675fff699d8ed94d43295f64ec28887a *src/ipplr_c.c
b0412c003b0b639cfe9481b1d2d67152 *src/ipplr_c.h
aa8f47e065d4eb691aceec8959d22b14 *src/multimgmos.c
5f02529981c33382f84200a74ab5f05e *src/multimgmos.h
76127b7ba4dbb1545a7fd21894879a32 *src/newx.c
7dd93c022ac5b2e501a05374eb054f18 *src/o8comm.h
3a366979ea1da0d7cdf6c50df8500f8e *src/o8cons.h
c29daca8cb64cadbec52358a9ffe0d5a *src/o8fint.h
b43da9ebe38f1f34a894989c013df065 *src/o8fuco.h
67d5262b9ccd821b753e67efcdaae3ab *src/o8gene.h
465ae878e5d5301725ede1c9bab751e6 *src/o8para.h
8bda49e6d3051e888393b328ee3d053f *src/pplr_c.c
3b6ed04d9897d9ebf80f4527cef664de *src/pplr_c.h
19315299f728a9603a3c2fe61ca134c2 *src/pumaclust_c.c
55f8b829ff5c72a92be95f10623de2a7 *src/pumaclust_c.h
3b507b92f42dba77c33f11b65aebe6f5 *src/pumaclustii_c.c
b5d6690a2c677c9d60d84c954492236a *src/pumaclustii_c.h
71af9fe8bdca16bd0a59e6ac6c5dd9ce *src/user_eval.c
11439dd7bd8692eac20034ed9e252190 *vignettes/changelog.txt
4393cd964e96b44cc5905d50198f7d47 *vignettes/puma-014.eps
6e53a382130205531ac419b606bf4368 *vignettes/puma-014.pdf
6bd0fa130b14787fd316d5af18f1cd6d *vignettes/puma-015.eps
2b64a63c039935fe07b805e9a824990b *vignettes/puma-015.pdf
eff72c3fda9e7dd48e5f8a6c89432502 *vignettes/puma-016.eps
7622d90254f2f9432f78127981bc115f *vignettes/puma-016.pdf
0cf1de95a25b9475825820c0bacdb665 *vignettes/puma-022.eps
e153addad43f47e1d987d3125de9dad7 *vignettes/puma-022.pdf
4300eff4bdeae67ce9674dc007729b0f *vignettes/puma-023.eps
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e5d339aa32f256c7fcf217f49b665dab *vignettes/puma-024.eps
6f15c2ef873d2768723d7eb77bed5c8a *vignettes/puma-024.pdf
065461b57d8e7705c9c2431314a175f1 *vignettes/puma.Rnw
1f057bf55011455d08f32f64333f6bb6 *vignettes/puma.bib
