9a788d8b8a5c9f602c4267adb3c0d4d7 *DESCRIPTION
fa27e6602ae848650141f8e8b2224dd4 *LICENSE
2d679b75fdbd41d835b0213229649924 *NAMESPACE
dc499373cb679443dac369d62e9031e4 *NEWS.md
4a399549c6d67a7e32a7b560c0b5cf5f *R/DccMetadata.R
23bb44fba064f1d7e1921906205c76ee *R/NanoStringGeoMxSet-accessors.R
ef4c340a987a86e30a38c2c4061dabcf *R/NanoStringGeoMxSet-aggregate.R
70e1fda05e5e6a5c60bf82c33d990d4f *R/NanoStringGeoMxSet-autoplot.R
6ee6bbdca94a348ee8c17c027a42dd66 *R/NanoStringGeoMxSet-class.R
38aeb4c76de7fdd2a460d016d96e3bcf *R/NanoStringGeoMxSet-de.R
f11f54411ce107e6d0d9660490c84a10 *R/NanoStringGeoMxSet-normalize.R
f000fd3546df086b1b195cb3f3795556 *R/NanoStringGeoMxSet-qc.R
0fd5052bc1d41e02178f0467813e9f79 *R/NanoStringGeoMxSet-signatures.R
6aabf286f4e497c9b9a4c6137b3afbff *R/NanoStringGeoMxSet-validity.R
866272f3c858b327fae9da200c3c5748 *R/coercions.R
db4f1aa06f9cbccbff9aef345cc2c4f0 *R/outliersFunctions.R
f3a3064d3eae24b100f0de0a9827c2f4 *R/readDccFile.R
87c9e40e17154446ddabb235b844fd9f *R/readNanoStringGeoMxSet.R
df4a365e9c8e63e6da0aca86cd8ececc *R/readPKCFile.R
9fef31ab990af4c75c2457fc64d69fb5 *R/utils.R
ee3856ae93ac3a87b5a4c4cc57d36cb2 *R/writeNanoStringGeoMxSet.R
1264a1c4bf13b587c9d5c4d5a94596ea *README.md
d69297cc219ad33ec4e46e8aca711ce1 *build/vignette.rds
6625a3da48684341203f2cfa0d102eb0 *inst/doc/Developer_Introduction_to_the_NanoStringGeoMxSet.R
4199c59fa136be5d617f1cc6861843a6 *inst/doc/Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd
5cf74887c790cabaa743123e0ff3bc64 *inst/doc/Developer_Introduction_to_the_NanoStringGeoMxSet.html
53e9aa63b816e7d97f6474ccdb038539 *inst/doc/GeomxSet_coercions.R
58bad7ee090e3404bd12886328364249 *inst/doc/GeomxSet_coercions.Rmd
589019e6d98b65efa530d246965c1316 *inst/doc/GeomxSet_coercions.html
a7faeae7a2ba9d23c5044733b3ca5187 *inst/doc/Protein_in_GeomxTools.R
2164ba05a93ee9821751befbc6c0ff1b *inst/doc/Protein_in_GeomxTools.Rmd
29f171c823259d56c3fe2b009b992b4f *inst/doc/Protein_in_GeomxTools.html
ad9e0097323f85a6d5592514fe5c25d6 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A01.dcc
c504e2d840e313020185807a9b36a687 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A02.dcc
9e475e2922a93f5272170d9f82b4ac07 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A03.dcc
41df6592149c679cf747aa9c2ffae76d *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A04.dcc
fb5f17918049f6fd1d23b6fb88f614bb *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A05.dcc
3f84d6fefc75d56d879931e490642914 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A06.dcc
fa692b83ad487aa6823608981f3c66c5 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A07.dcc
36fe7468169559947f24cb8c4c14cbad *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A08.dcc
865ec61f366d7e66e6f876070116354f *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A09.dcc
fed9eb6216cbb3086fad19ec71535507 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A10.dcc
acee4a0a3ad86a5e4efc1018b845f1ee *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A11.dcc
1c4457044cf01d668f14b4ccd0bd7bb7 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-A12.dcc
c789946f957d354ebca8ae536611008d *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B01.dcc
c69e50e1db9095b5a20c7f16085ff9d8 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B02.dcc
59d31b3009ab9e3f58bcc8b7265dc33a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B03.dcc
0d98703575d1fbbb2da461ff136d7f1f *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B04.dcc
a2a5e5f094a0beb5aece9db56cfdb887 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B05.dcc
4e9bec56d24bc319ad1e4421c0a36fb6 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B06.dcc
f0bcef34a9caa844256402f2a5f4e3e0 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B07.dcc
c6d6afd96944ec8b9312e7cccd567df9 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B08.dcc
b15ab97cbea33931103fed6fad699d76 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B09.dcc
e65ca4280639e706d7b20f5dd593c7b3 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B10.dcc
1a7cbd46f16ec3d87149f9c4c644298f *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B11.dcc
4dac39e119d38f8177839c24b10bf704 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-B12.dcc
6f85a98310bf00bd91688b7ab87f7f8b *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C01.dcc
c1c50b29dbdb52b4feda8c23e2bb7667 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C02.dcc
c2da37d8560053377dd84065353ae565 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C03.dcc
2cb22bca50078107593652f5e3880372 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C04.dcc
d3626c9081bf3748a024bd633c2dd01c *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C05.dcc
eb7fe11d82912f7a6ec59a1fdbefcd27 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C06.dcc
34b13bf0a47932170ab17159bd71b5e9 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C07.dcc
d0435da4932f757ae82ad1c04e17b4d9 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C08.dcc
30da9bb937e793ec2f4ce09c2de23f8e *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C09.dcc
70216685ba183c8133ec8c6c27001507 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C10.dcc
216a6476e63c4a6fb545652d4dc55059 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C11.dcc
7ae324180e7b8b47f2e324d5f55572a0 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-C12.dcc
069b3dffc6f53638695edc44da3b5f2a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D01.dcc
82bc41e5b269c31125bbfb4bf6499218 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D02.dcc
9554549815235001ed38caafa4c07bcd *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D03.dcc
ed765b6059e88c9f2f1f62121255001e *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D04.dcc
295331b3d05b8f0bb3d6051a7044c407 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D05.dcc
db886bb5cb72de40e01cf39e78da1231 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D06.dcc
472a465dbf2573dedd37b9868370a281 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D07.dcc
a56e68f5f306d73c588bb0b39d88c74c *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D08.dcc
543bf6a80de8d6cd95df3ac18a63a720 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D09.dcc
c72f9b1bee92ccdac8dc92415e8f802a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D10.dcc
5c620990a0ef7fea541f8e33176c4d39 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D11.dcc
6fd536c258272770e22152174ef062a1 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-D12.dcc
373861767fc79a355d500cae14102b16 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E01.dcc
3c1b6a2c01c72d561059853eae95905c *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E02.dcc
712b1c2974519bb02221dfc3d8bff857 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E03.dcc
9a357e312f9e85a17b4e0eec6edf6222 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E04.dcc
5b38454822342c581d1aab5abed8992a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E05.dcc
d94d22fee27626f7881ead8ef91c92fe *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E06.dcc
467e2317cc043976c160f2e80c7a0b15 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E07.dcc
3679a63dbd574866222056f05e1b579a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E08.dcc
714997a663bb3689a23de34804d8741a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E09.dcc
15e04603a78f693480f6d302e122c40a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E10.dcc
db273943ed4e597ecb4154b9882d729e *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E11.dcc
8fc79fd5829026b86d1dfb059c44473a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-E12.dcc
0d4bf3c1b07d6c9178f295113ad9f6f6 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F01.dcc
481c749071f61c2404367223b8c15e54 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F02.dcc
ce5db4d94f399a8f434bc7eb066ce57f *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F03.dcc
ae281fc728900c61f47c45be8ff4b7ad *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F04.dcc
c16f08e91e20483f1d6915bec751c4b0 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F05.dcc
aff8f1578c229f1b17499cf419e2f4dd *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F06.dcc
7764a04976c21b692d41806d7c3aef99 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F07.dcc
53b4ea74f7cf9582fa573e100fb88d6a *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F08.dcc
436b328243a3634374f42298ea9f73f7 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F09.dcc
dac7296bbbcc0d497a97ac5ec42ac3be *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F10.dcc
af1815f424ad571626168d9c2d8e59e6 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F11.dcc
94c529dabb8758bc90ee8410d4178f68 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-F12.dcc
e487a1b5216712fd815aa098e8b42330 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G01.dcc
e37dc0b53b7576779d0fd79ffe30ce99 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G02.dcc
0d399dedc1c301771e3dde402129f68d *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G03.dcc
1630554c3988bcefeb8c2ab7dbf4f115 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G04.dcc
b5322164dd76fc52819258af22a8f2ff *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G05.dcc
33f7218170fc5f310a5f918c04e6c7ad *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G06.dcc
47a8b15572717c5d59cbdf4c280109c9 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G07.dcc
67e6be9dbc77206569d0f1d532630443 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G08.dcc
50700cc89489db496f7a7e40ab81ade8 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G09.dcc
b16f83722f9f38dd43f23f2de92b71a3 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G10.dcc
ba12cd0e6ba0889a39a07e895c0dac45 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G11.dcc
d7672c3c1d1829eff97fbc63dfa5ce89 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-G12.dcc
07034f72e2ccd32d5ce32f0a91d9dac8 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-H01.dcc
f212094656cb6adcf1f69d435e2709a2 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-H02.dcc
954e2e00668f44efce7e8ad6547b35be *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-H03.dcc
004c8927f1cb14980357118e3391e92d *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-H04.dcc
6b096c50ea2869a0b4943e35fd3fece0 *inst/extdata/DSP_NGS_Example_Data/DSP-1001250002642-H05.dcc
a3e622c88bc67d05262a0e6378baaac4 *inst/extdata/DSP_NGS_Example_Data/GxT_testing_labWorksheet.txt
2fdaca0e45a827272159b226a11b8ab1 *inst/extdata/DSP_NGS_Example_Data/annotations.xlsx
77908de9afae4f2f77d7d8d469e7b576 *inst/extdata/DSP_NGS_Example_Data/demoData.rds
6ab54a9100f63327849a6875a960c43f *inst/extdata/DSP_NGS_Example_Data/fakeTesting_config.ini
38e730df6fd16f1afac8d4d26c5fb5fd *inst/extdata/DSP_NGS_Example_Data/pkcs.zip
cb7ad756cc2a498624ecc17b5209d50e *inst/extdata/DSP_NGS_Example_Data/version_example_pkc.zip
5f36e63f3c3c422ffc6e0f3f9258552f *inst/extdata/DSP_Proteogenomics_Example_Data/Annotation.xlsx
3f2f8ad64da45d516addaf4e06a354bb *inst/extdata/DSP_Proteogenomics_Example_Data/DCCs.zip
c1491f29677dc50d80c3a5ff56863337 *inst/extdata/DSP_Proteogenomics_Example_Data/pkcs.zip
cb5db90f53bacddb6123c1ab928a6747 *inst/extdata/DSP_Proteogenomics_Example_Data/proteinData.rds
26437e3d9ff11987557a2505c60ceb78 *man/NanoStringGeoMxSet-class.Rd
2d3f8184dc2036beee4e40ddae382148 *man/aggregateCounts.Rd
8dd40c5544c084bd4489554dfd9b7042 *man/as.Seurat.Rd
5ed4519032491d7129fb70d4c79b77fd *man/as.SpatialExperiment.Rd
f6a95bb9fa681f3327d2a8678332a36c *man/checkQCFlags-NanoStringGeoMxSet-method.Rd
73be8e5b93de45dc5818cdd550c397a1 *man/checkQCFlags.Rd
2bd32e5b9fd2b2074e1726c1e7e7295d *man/compareToConfig.Rd
84f502505c6614f77887001e87afa64f *man/computeNormalizationFactors.Rd
f5bc5d86107073d24af35a929de55e62 *man/countsShiftedByOne.Rd
56bf834b3fa5175547c4bc4cb0f3e381 *man/hkNames.Rd
d06e3799b5bfb4e90937c14ba815198f *man/iggNames.Rd
8852dd39176aa2a1fb95e1353a6c9e18 *man/logtBase.Rd
1abcd2bc1029ab8f19e85743e8afb659 *man/mixedModelDE.Rd
3125e787b381d03d692ffda621413ac5 *man/ngeoMean.Rd
9ec0a3a846969818e683e1737a1f268a *man/ngeoSD.Rd
28614fc64bcd1f580f6806f6410d5b35 *man/normalize-NanoStringGeoMxSet-method.Rd
4272d8b3092d4750fd5adac50497754e *man/plotConcordance.Rd
a9fad2001b5d5d6862f22cbfb46c1bcb *man/plotNormFactorConcordance.Rd
6079a3e129f9421d8d3bd72dea1b4b51 *man/qcProteinSignal.Rd
deace38c87866a92570582a1a9db9383 *man/qcProteinSignalNames.Rd
fc2d11198e766a1c88660919fceeca37 *man/readDccFile.Rd
0fd24133c3eec0621974b7f3d4cf29ca *man/readNanoStringGeoMxSet.Rd
82be9e6ad88d10d7107f831ae82142a0 *man/readPKCFile.Rd
a3db7bcb1552cba56718fa1b782b786e *man/setBackgroundQCFlags.Rd
f76d9235936b6b54b8c3293d6b8870e1 *man/setBioProbeQCFlags.Rd
cd912fc044bcaf501e3f8d1e1fb81ee1 *man/setGeoMxQCFlags.Rd
a144f34d7481c89f9b7aa98c28f31802 *man/setQCFlags-NanoStringGeoMxSet-method.Rd
e6b4180df053f9e3bfb17767e094c019 *man/setSegmentQCFlags.Rd
4d056db41cc42e4c3c9a14adb564516f *man/setSeqQCFlags.Rd
3014c2d73c0d59806a794906e1e1223d *man/shiftCountsOne.Rd
6db523ee933719792309a7c2b7b0611f *man/summarizeNegatives.Rd
7237b596a3d92642ebac1e9be8536848 *man/updateGeoMxSet.Rd
5a3f2fd47b6a398d25679a784e66ab7a *man/writeNanoStringGeoMxSet.Rd
83d5d92bcbdda7d79269a99601f8fac3 *reqs.md
eb8486d9b621cbb6870ed1b5d54b066b *specs.md
b3da6a3c0487b6d6b0a61795df33faa3 *tests/testthat.R
d9d5318bb20ed9473b3344bded395f9f *tests/testthat/testData/GxTv1.0.RDS
0db1044e73b193f692791e547aeeff2e *tests/testthat/testData/outliersGrubbsTest.RDS
16ff456036f36bce57db46f0e63640a2 *tests/testthat/test_GeoMxSet_accessors.R
dd5d1d9237a695fb8234adb60f941475 *tests/testthat/test_GeoMxSet_probeCollapse.R
c2820ba5ba1d40425cf2b78bc6273715 *tests/testthat/test_GeoMxSet_replacers.R
2d1ea4b4a0e2f94dba760406bc73d221 *tests/testthat/test_QC.R
390dac9dc0677858d4f774e69f9a19b6 *tests/testthat/test_coercions.R
42b9e30db65b1e213e76d495e2344ce2 *tests/testthat/test_de.R
f096a01b75afb2c9b76f554dfc8964e9 *tests/testthat/test_normalization.R
effa1311700d822c6e59fbffab3b0b76 *tests/testthat/test_protein.R
09cb153a5576fe91212d12cf1ff5307c *tests/testthat/test_readDccFile.R
a410e609c260816d38622f3c93229ad2 *tests/testthat/test_readGeoMxSet.R
f66b86d911d9b4c944c5c14597f5fd3b *tests/testthat/test_readPKC.R
fd6efb976f6d0e41a7b832eca4c1bab8 *tests/testthat/test_shiftCountsOne.R
4bfe27c36d66e25b5b1001cd768e72cc *tests/testthat/test_utils.R
78dea0b5a16309a7ac364ee3d59ccc37 *tests/testthat/test_writeNanoStringGeoMxSet.R
4199c59fa136be5d617f1cc6861843a6 *vignettes/Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd
58bad7ee090e3404bd12886328364249 *vignettes/GeomxSet_coercions.Rmd
2164ba05a93ee9821751befbc6c0ff1b *vignettes/Protein_in_GeomxTools.Rmd
