5df73109ab65abe732ff0d81736b337a *DESCRIPTION
f55abbf39b8b2cc691a34f0149e49131 *NAMESPACE
40931e34fe227484dda435249a764484 *NEWS.md
762c47a5d27df4232b107f411856e68e *R/CoreSet-accessors.R
ed2f370403295fecb33dda728c2132e2 *R/CoreSet-class.R
40e4d3f289f52703887e4fc84fb88ff6 *R/CoreSet-utils.R
4d1d35f55bf140df54dfc577b96ff47a *R/DataMapper-class.R
ba0b2b2dd2ade961e1b234ae1ee8c64e *R/LongTable-accessors.R
d3d66aa046be4fa187fbd85da6a994f9 *R/LongTable-class.R
53a09cb3ead4335f4780d989c8779dad *R/LongTable-utils.R
b5689046652282b0ebdc525d2665730a *R/LongTableDataMapper-accessors.R
79365bc4cdaebbfecb4e8870aa0e7e62 *R/LongTableDataMapper-class.R
b04fc73ab9e889d2f2982173b10b6f38 *R/TREDataMapper-class.R
1400c485c9098951df30b8059693db6a *R/TreatmentResponseExperiment-class.R
25da49f246b268ab523a9957846a0ab1 *R/adaptiveMatthewCor.R
6d241ca04101ab125fcb3d3c2c5425bd *R/aggregate-methods.R
787b3bcd84732d20d813c1565b7958ce *R/allGenerics.R
d28fdfd7532cb4cc47a4c0f7a2ac70cb *R/callingWaterfall.R
8111eb66c7d07540df2b98344408335f *R/connectivityScore.R
42cc5e8f18f993e310b0863a7bfbfeee *R/cosinePerm.R
7598c855a72877e7388ba6da16a75002 *R/datasets.R
d952120f93495b3a0693f6833cf67c3e *R/deprecated.R
a4b9a6507dc90ea861d74868bf36221d *R/endoaggregate-methods.R
98a49235bbda7470879d8de68fe00023 *R/globals.R
7371e389699853431682e77dd77c474f *R/gwc.R
9c26c1b2f12dba3cf71939c0fa3c7502 *R/immutable-class.R
135d602330e439759449b79de31ce9d4 *R/matthewCor.R
2eebc05a712688a2c074b76a2b81267a *R/mergeAssays-method.R
7036c2a86f5ecb03e8f9c7de67edd44a *R/methods-coerce.R
cbb22bcffa55d22645400866694305a6 *R/methods-dim.R
11c5e54990fc029743028ace21228a51 *R/methods-dimnames.R
6e63297719a1d92459d0a94876b52635 *R/methods-drugSensitivitySig.R
e9b7cd5fc89439d34b47935bfbf725b7 *R/methods-guessMapping.R
f4c40d6c3c7eb623742f7349b069106d *R/methods-metaConstruct.R
1278c18a2b50aa3ce68de6ef331b8785 *R/methods-subsetTo.R
4cb544439c02b229b3d4cd3315e8a1a0 *R/optimizeCoreGx.R
dafa24c28525d638b0d6b2f295c5c19a *R/updateObject-methods.R
6672016840a0adcf6e1bd1040bc8c2a9 *R/utilities.R
1bf2e3074f424989e00e811df4205d22 *R/utils-iteration.R
1a60b9e9af00792cc1055f4aaa251b28 *R/utils-messages.R
7aa7fb3902e14724c207f6ccc368b3c5 *R/utils-optimization.R
7685f64339004fbf43e88a88a4919197 *R/utils-testing.R
7ffe75f2900520f4ce4ceb0454c781ef *R/utils-updateS4.R
96e8e398d64a56e7f09a054abb9d0d15 *build/vignette.rds
093367b4a20aee69754fddcfec9dc8cf *data/clevelandSmall_cSet.rda
fb1e6e25b4ba5b0f7b8134ddafd678eb *data/exampleDataMapper.rda
3547520cf610dbc67823d665fc221bae *data/merckLongTable.rda
6362eb312ffeb85caf6b917a7dccd79f *data/nci_TRE_small.rda
8df19bb65027a94a6d2935755fc30231 *inst/CITATION
a9d9e77fb7960a6a0b8aab668877bec0 *inst/doc/TreatmentResponseExperiment.R
9c18629774d6d2fa0597f049af70bc16 *inst/doc/TreatmentResponseExperiment.Rmd
1ae382a19c7e07da6c7beedf7cb6e292 *inst/doc/TreatmentResponseExperiment.html
deeead02c2184840fd57fa9a64c10566 *inst/doc/coreGx.R
8a19f2ffb2d9eab7f1acb13f76e042b9 *inst/doc/coreGx.Rmd
4a58c568218b7c97930eaf477d0ea0d6 *inst/doc/coreGx.html
908d286e85326963a786a121d81fad9d *inst/extdata/merckLongTable.csv
3f9c66b998d9e2b20e79d68b9f041aa0 *man/CoreGx-deprecated.Rd
c816bf2eb9dcfea3f82323fbe01eba25 *man/CoreSet-accessors.Rd
254772b276d44d40a8e66732039e238b *man/CoreSet-class.Rd
810e067f4f05e8377a54497612f92afb *man/CoreSet-utils.Rd
469970285fb8dd5a9681d42a0b2b9bfc *man/CoreSet.Rd
63bb3017e61ebdfddaae544a2f26b907 *man/CoreSet2.Rd
73b56edb616a62ff039d9435cef37b51 *man/DataMapper-accessors.Rd
07a1d381eaed5bf9c8a0312523224ae7 *man/DataMapper-class.Rd
6a025ce35d1ec46caa99b15f5da6421b *man/LongTable-accessors.Rd
0fc5f6927d07325f7595b083af10265c *man/LongTable-class.Rd
84864e239d1e90c3ed9014c78ddfecf4 *man/LongTable.Rd
34e4e0600c27f0f593884fe10a5a46fa *man/LongTableDataMapper-accessors.Rd
0730000516071cca23151466403188df *man/LongTableDataMapper-class.Rd
c2bb60961831a1af7aaccf9a7040f613 *man/LongTableDataMapper.Rd
a5b51400edaf0a0e9b96f30ccf0c222f *man/TREDataMapper-accessors.Rd
bf52687c8c844da2f63930ce38f57e01 *man/TREDataMapper-class.Rd
f45f1c403c138e9bd48e7078ee251d60 *man/TREDataMapper.Rd
b225dcc91f4fd8b578acbca23ef08a79 *man/TreatmentResponseExperiment-class.Rd
f99fe474784b1f3d274f097381cf303e *man/TreatmentResponseExperiment.Rd
aff261cbf124217b540e90a8295f4c30 *man/aggregate-LongTable-method.Rd
9077204f98e1accd93fcefcfeca7bc02 *man/aggregate-data.table-method.Rd
a19cd86d63b0dd8186118412c3544d46 *man/aggregate2.Rd
eb41ded8713beaa4d749eadc569dabde *man/amcc.Rd
cdf107469455aa052669ea1969c68784 *man/as.Rd
67befb1b271c099a8dbe692cfb122ac6 *man/as.long.table.Rd
396137c6e4bbfab5505e4f6ddb9d630c *man/assay-LongTableDataMapper-ANY-method.Rd
93e125b5b18cc1b9ddec1c8c4cecaec7 *man/assay-TREDataMapper-ANY-method.Rd
dffbcfc3a238997f6167696f5eb825d1 *man/assayCols.Rd
b696dd7f11c104ed1e063cc764e9cb65 *man/assayIndex.Rd
f73fda5318fbdfe360064c21af5808fb *man/assayKeys.Rd
b1e61ca49386e8df7308e1fa30c5efc4 *man/assays-LongTableDataMapper-method.Rd
82786d537487bebffc0d15af0c8d2e38 *man/assays-TREDataMapper-method.Rd
f46501c6023f53306c5bd090e31edc43 *man/assignment-immutable.Rd
5b29c6ebc0fdaa898a40fd51dd67deff *man/buildComboProfiles-LongTable-method.Rd
0393d37fea6fe303b5282d945e1b250e *man/buildComboProfiles.Rd
9724801c9721339389bf0a26dd42f465 *man/buildLongTable-character-method.Rd
3ab3cd636d23bfcb4d89661aad5012ac *man/buildLongTable-data.frame-method.Rd
ed98c05a31ad8c9a177306918466e1d4 *man/buildLongTable-list-method.Rd
d5be9d70955065ced6cf053eaff3692e *man/buildLongTable.Rd
689f9a57f2e3ae1dd8ab46eb03c2f7df *man/c.immutable.Rd
5cad68ce48744dd78a24fbd454e64014 *man/callingWaterfall.Rd
26c5ec3fe16f0154a76c493845fa975d *man/cash-LongTable-method.Rd
f38272926be7870e965ce9205406e099 *man/cash-set-LongTable-method.Rd
58d8f9602786b0427f0253d5f14821db *man/checkColumnCardinality.Rd
17455f44abb33a6f4288df5bd555019d *man/checkCsetStructure.Rd
ecc6c0c82b50cbf49e06798716cbe073 *man/clevelandSmall_cSet.Rd
57930623c140d447c24a46e94ae61d3f *man/colData-LongTableDataMapper-method.Rd
4147a863ade4065b598476858c68254b *man/colData-TREDataMapper-method.Rd
9d20b6092effdaeaa969a7689abd5436 *man/colIDs.Rd
df1a6fefe001df27138c7740e0cba82e *man/colMeta.Rd
32d189dae5bb85eb1f346e0a4fe0495c *man/collect_fn_params.Rd
fe4361b2aa020c24eb7988b2dc4793a0 *man/connectivityScore.Rd
12032adacf90e440aa2d81a9801e85e0 *man/cosinePerm.Rd
6d043fadb1fde065c29a7f46e3e4067e *man/dot-.Rd
413774fd29fb5bc748f0b1414825faa0 *man/dot-assayToBumpyMatrix.Rd
dcf54361ef800dca9b35a8f78765d3d5 *man/dot-convertCSetMolecularProfilesToSE.Rd
a7d37f5fc50ba775b41069ac14e0743e *man/dot-distancePointLine.Rd
4ff2a47ffc332b20b0f4506c0f2bea3f *man/dot-distancePointSegment.Rd
c8fb3b3b649b39da84c3e205a55ccbec *man/dot-fitCurve2.Rd
b77c54aa9c18aef52023b808639f0cf6 *man/dot-intersectList.Rd
21471956af287c2098647f1d25d31365 *man/dot-longTableToSummarizedExperiment.Rd
678677347078e28f64df1b94594ab961 *man/dot-symSetDiffList.Rd
487144348986cc304e1fb1743392c879 *man/dot-unionList.Rd
93ec796b22e72f8ce3569cf8fc3800a9 *man/drop_fn_params.Rd
63f534d6675fcf7201f4372a53083501 *man/drugSensitivitySig.Rd
3163c8a40c3f54c2db8297b4a8954031 *man/endoaggregate-LongTable-method.Rd
4dfd47c7904a3c21f6fc912bb377fe0d *man/endoaggregate.Rd
5074c32c042082a7e33730f229df823d *man/exampleDataMapper.Rd
ca8845704f396bfccb4c8671dceb7f84 *man/getIntern-set-LongTable-immutable_list-method.Rd
f0745fe0f0675686b519938c4f0cf633 *man/getIntern-set.Rd
c093b011e3775ba14f83c38ff7bbe538 *man/getIntern.Rd
b15a017e27379338b80f223a687cdd53 *man/guessMapping-LongTableDataMapper-method.Rd
f870c16d8d46d26eae57ef27b9738673 *man/guessMapping.Rd
ea0b673dfa19357739b3cc80536f63f0 *man/gwc.Rd
eee1a56524e59c075c71777c3c7f7ee4 *man/idCols.Rd
bbfd4864261ed2ab924d236a8cec6ffd *man/immutable.Rd
19a9af55721c07da3471825aa973821c *man/is.items.Rd
a3786d6c64f4bd447dc1b1e2f4b0c122 *man/is_optim_compatible.Rd
a2c3f46aca790fd09fc93f2d4e3b0969 *man/lapply-MultiAssayExperiment-method.Rd
c191be4aa1a13f1d661bb2b2c15aa81a *man/list_OR_LongTable-class.Rd
0ae8d590c32d594343bc74ef7faf01ed *man/make_optim_function.Rd
a52536983ae05b1427616b67a27a0bbb *man/mcc.Rd
df1040dba4ac9a95c31d1e046a41be72 *man/merckLongTable.Rd
9b8440fc8d9fece577a2b80425c429c1 *man/mergeAssays-LongTable-method.Rd
b78a1da6e03a9378d2a6f73ac09075d4 *man/mergeAssays.Rd
5619fb3d73d2a4b63df647d34f67a3e0 *man/metaConstruct.Rd
8df5110a1a4ac23b6e9ebde11dae3514 *man/metadata-LongTable-method.Rd
959018f70726e0be8a592d5ffd82c24a *man/metadata-set-LongTable-method.Rd
ae8a51cc6297460bbc9823d96d388ec1 *man/mutable.Rd
3d9662cc6540e082c8d78b775d57cf5e *man/nci_TRE_small.Rd
c8f685844a1ba67f11677d34844717bc *man/optimizeCoreGx.Rd
8b7f3f03891b316ab69f6a8d05dc6832 *man/printSlot.Rd
e0ecd9e42971d728d6b55d8621af8a54 *man/reindex-LongTable-method.Rd
1ee65338f4e812af2494f47b4ca007b6 *man/reindex.Rd
eff9ff6d59e9fb73823a4690cd1bf5a0 *man/rowData-LongTableDataMapper-method.Rd
b682a7587e62e7159854d5603fa12e95 *man/rowData-TREDataMapper-method.Rd
e07da529b11112c2c4240e8ff7d7b3e4 *man/rowIDs.Rd
aea89d4240f679e810c0b5de10bd62bb *man/rowMeta.Rd
30efe91d4b089a94957b436a7111897c *man/sensitivityInfo-set.Rd
8e0aa05fea3ebc3408780eff169191f8 *man/sensitivityInfo.Rd
b519e09f1781ad25240023d09b3aa75a *man/sensitivityMeasures-set.Rd
64857fa1dad835f70cef08a5f0afb3f4 *man/sensitivityMeasures.Rd
81df70ff04c232bca08526b4c2b94797 *man/sensitivityProfiles-set.Rd
4d7854d593b2783325a730a3b4acdca3 *man/sensitivityProfiles.Rd
b424728ef6a7488c29f967c408ac18f6 *man/sensitivityRaw-set.Rd
5142a43e7095c696c23b72e6348ffd51 *man/sensitivityRaw.Rd
0eb393a0dd16ef747ed3641ff1dd7a41 *man/sensitivitySlotToLongTable.Rd
148450e97d8bf0ca3747ce81a55f6129 *man/setOps-immutable.Rd
73f7dbb9e1b012fb10ac1b7e0c1e0b6f *man/show-CoreSet-method.Rd
05e639cdcab816bc46574f613bed9ac7 *man/show-LongTable-method.Rd
ebf8fde0c2ef0dd087f11ae011f94746 *man/showSigAnnot.Rd
2caa0094074a4549f21644e65c5e2460 *man/sub-LongTable-ANY-ANY-ANY-method.Rd
1f57353271d479111a204218f6471bc2 *man/sub-subset-LongTable-ANY-ANY-method.Rd
a88865014f9e6516e115e3bc9b7f702b *man/subset-LongTable-method.Rd
a22dbd20d036b41606b02221e2278dc0 *man/subsetTo.Rd
dd89dba4f4c37384045c6dd1e74370fd *man/summarizeMolecularProfiles.Rd
854840e217a51c68400a4762420fe838 *man/summarizeSensitivityProfiles.Rd
847d67a8eb425b3c2734bea41a0f4c7d *man/updateObject-CoreSet-method.Rd
422b0ee1328cb8df83f1b973330e4fa8 *man/updateObject-LongTable-method.Rd
abba17bb61771e90be76904f8e12781a *man/updateSampleId.Rd
d1ce506f9840fe3ca588872f8559c587 *man/updateTreatmentId.Rd
d085d9375aa41205106274c0c4e4c484 *tests/testthat.R
eae50196d49ed4ea4211591144a1a56c *tests/testthat/test-LongTable-accessors.R
59d80abcdd8377c594b7b38db86d2bd5 *tests/testthat/test-LongTable-class.R
9d38acc4dfdea09d6b2b8d5960ed96b5 *tests/testthat/test-LongTable-utils.R
ac81e4f22a8ed5656f2054b642ed5b40 *tests/testthat/test-aggregate-methods.R
6a18f2f1bcc7a909a6cd9717479179ce *tests/testthat/test-utils-optimization.R
9c18629774d6d2fa0597f049af70bc16 *vignettes/TreatmentResponseExperiment.Rmd
575f85edd15f857e3e0968623958a2ff *vignettes/TreatmentResponseExperimentClassDiagram.drawio.png
236e1d0438ae3f380be078df7ce00126 *vignettes/TreatmentResponseExperimentStructure.drawio.png
8a19f2ffb2d9eab7f1acb13f76e042b9 *vignettes/coreGx.Rmd
