2e985bf321138a9353a21652fba32bf9 *DESCRIPTION
7775337c6e10c237b19b17abec40bab1 *NAMESPACE
49fdac3e956f49e15b8c65d49b790b56 *NEWS
43da88403b064edd211bf2cf07ef140f *R/2AllS4Class_ProfileParameters.R
bef465fb850e5476956aee75fa90e410 *R/3AllGenerics.R
b29c7f413a7f8afc6fc6653492f3461d *R/4AllMethods.R
1a2eabe937ae43e188eeb5128bbf3381 *R/AllInitialize.R
59a1943c5d48aa4bf6fe5ad37147c571 *R/AllShowMethods.R
4dbda84122736cfbfc709f2f9d3b6873 *R/DataPreprocessingDev.R
c6f13098828fbd11be88aec26cc00571 *R/DataPreprocessingGenericFunctionsDev.R
75dff6b8df06f89937b19b0ce65630e6 *R/GAAnalysis.R
ce53a34081cf90c338bc00ba0cb2e4a8 *R/GAGeneric.R
9f084c3d5d1efe4bdf93a8ed919f0f8a *R/GenomicProfileGenericFunctions.R
4aea3513ab653997198113a7c102456a *R/computeChIPProfile.R
d24303fac0f6badc2c90678d4a0362af *R/computeGenomeWide.R
09eff857aaac16345067269607ee614a *R/computeOccupancy.R
ebd46afaa6f8d7c883547b093c86e7bb *R/computeOptimal.R
ce016ca8c97a8c95480774f1d4cd8bb5 *R/computePWMScore.R
578c2d048342e359de13ca0342007baf *R/parallelInternalFunctionsDev.R
3f17e8f1b1bfbfe4768e36a289b6a469 *R/plotOccupancy.R
8ec042c6891decddc05cd9b9b898e190 *R/plotOptimalHeatMapDev.R
f38ec64979eec358b545163f8fd84b2b *R/profileAccuracyEstimateDev.R
d7cea4b636bcd0404b6a21dbfd78c6d9 *README.md
0aa707562d542bd7bbe1522d2fd440d6 *build/partial.rdb
c9825246cc3396debc249f5cfc61c5b8 *build/vignette.rds
5ad8bde13480b15f02e67253e7b216fa *data/ChIPanalyserData.rda
0b9b887e498e36ac8be41f9202b9580d *inst/CITATION
4aeb17d8194ed96e86adaad0c4d403d3 *inst/doc/ChIPanalyser.R
a0a0bb7d330a5d93dc1b118bbfe5c2d8 *inst/doc/ChIPanalyser.Rmd
e3612954bfa84fcfedfe866aab04b95e *inst/doc/ChIPanalyser.pdf
df141137bac6665b55ecc8bbe3d25a90 *inst/doc/GA_ChIPanalyser.R
a0fe48e002e094f9d5687a499d0d008e *inst/doc/GA_ChIPanalyser.Rmd
6483a975dceb04cdeb4f80e759e3ae07 *inst/doc/GA_ChIPanalyser.pdf
0d2f740a6e7ace08f078a1584e7d3a1a *inst/docs/ChIPanalyser.Rmd
db0b855deb56ee2826898d1551db9ee6 *inst/docs/GA_ChIPanalyser.Rmd
8a3b43ca823f36236573ae7ea4a3a035 *inst/extdata/BEAF-32.pfm
e8e30dd7d90d9f97d171cafae3bccfab *inst/unitTests/test_Units.R
06a424e88dc2b4be8b0d3950cfb05e6d *man/BPFrequency-methods.Rd
2f75de51281943767648ab4784ec628b *man/BPFrequency.Rd
37586f3ea16e7756e22996e37a31f7b1 *man/BPFrequency_--methods.Rd
2fc64c59dfb37308ec01cd7f4cc279ac *man/BPFrequency_-.Rd
5038b46baf580f0fc5d50fd87a9d775c *man/ChIPScore-class.Rd
38bbe3e96158e947097a5bc0347a0d5c *man/ChIPanalyser-package.Rd
18c396aef47bdb077057720a23e6b03d *man/DNASequenceLength-methods.Rd
46807868aaad866c6d8ea756111690ad *man/DNASequenceLength.Rd
00944c1c815ce3138df6c63c9b8706d9 *man/GRList-class.Rd
b9a9b862eaea9296d8c13adbe8a7c594 *man/PFMFormat-methods.Rd
ca7621326b9a8498fad506165e99d8bb *man/PFMFormat.Rd
746839e855cbe4e45dcf10b619c221bb *man/PFMFormat_--methods.Rd
c2e8a5f234ff6df3dce758e92dd124c6 *man/PFMFormat_.Rd
3ed7ccb50e38c71b302cd79b0dc0278f *man/PWMThreshold-methods.Rd
fe20f78e011b6232edf3ff2d842a560a *man/PWMThreshold.Rd
246310f49f07296bd066b0514a7b99f6 *man/PWMThreshold_--methods.Rd
5ed02eefdf679d5282953be98a63a017 *man/PWMThreshold_-.Rd
f28856397afca1fe9369f8b4a1322c86 *man/PWMpseudocount-methods.Rd
dcd888b338f90f648c1284e07ba59d53 *man/PWMpseudocount.Rd
3aff1b76860b31c98d529e9979a2c9dd *man/PWMpseudocount_--methods.Rd
ec7f867e59244e4293a391bb6cf969fc *man/PWMpseudocount_-.Rd
063056beaad27d0803a33eff8b019f73 *man/PositionFrequencyMatrix-methods.Rd
636cb7aad666dc7568a5134f61cba2b9 *man/PositionFrequencyMatrix.Rd
a37d046a8cca00a1d305c021343207a7 *man/PositionFrequencyMatrix_--methods.Rd
391000e31f41ebe2f400beb01159dece *man/PositionFrequencyMatrix_-.Rd
874cb58ab1ae712fa0e409c6d9be0c2f *man/PositionWeightMatrix-methods.Rd
7af93dd365368f47f9d716ce45e3f7b1 *man/PositionWeightMatrix.Rd
92c67a4906f92d3c6186aaddd70de1cf *man/PositionWeightMatrix_--methods.Rd
43b02fb7e6023eeb79813a4609419aba *man/PositionWeightMatrix_-.Rd
664071ce2c584955c6f6bc6f3a505609 *man/averageExpPWMScore-methods.Rd
b4b3a692c8468d10abb06930b3e669c4 *man/averageExpPWMScore.Rd
6bb1509cc6d5979074ed8ad481475ed4 *man/backgroundSignal-methods.Rd
38fc86ce189a97532f890e51f0085914 *man/backgroundSignal.Rd
784b2a93c88d461db46361e68c42f117 *man/backgroundSignal_--methods.Rd
b213ca65c8bdb415a1f0c250bf90c8fe *man/backgroundSignal_-.Rd
53af604e2c167b6e897fac6c7f14c046 *man/boundMolecules-methods.Rd
7de62b91975ce95aef1f0ffbf0acc4fa *man/boundMolecules.Rd
1f44159d695fdac3f3aca78206672a18 *man/boundMolecules_--methods.Rd
541dc22499d30f70c1bd880f2c6a9857 *man/boundMolecules_-.Rd
2c0c3dd52da1dc483bc0dff38d08d715 *man/chipMean-methods.Rd
2573d3ca731d2ab903e81867884cbb5e *man/chipMean.Rd
95979a9dd4fcd70c0722beef994650af *man/chipMean_--methods.Rd
ad201c746e5e386ac704b934f950e9be *man/chipMean_-.Rd
04a99b39deba5e7f16e1e1935b291c5a *man/chipSd-methods.Rd
161427a8ba4ef8d2eba37684478c903c *man/chipSd.Rd
9162fafa68cf1230a25ac61601439e38 *man/chipSd_--methods.Rd
ef69d13bc4fc81fd6a48099f25ba619b *man/chipSd_-.Rd
cfceaa72ee5fc8a14ef98029242cb1ee *man/chipSmooth-methods.Rd
e61a2826c14720edc9028baea7687c02 *man/chipSmooth.Rd
86c17dd33c21135bc4dac77ef5d112a3 *man/chipSmooth_--methods.Rd
0aa69372b5872dffd76a47c3d178e003 *man/chipSmooth_-.Rd
a2f5e76a5d34d38eee7d9a916558a883 *man/computeChIPProfile.Rd
6dfb9628bfb5265255a2aad618bc7961 *man/computeGenomeWideScores.Rd
9f36ebb82113e8eef0304e140f0e9717 *man/computeOccupancy.Rd
4ab4ae83f72ce81d2d858e7a4ec0cc43 *man/computeOptimal.Rd
ff49be50ed451de71d4981f7308f6d1c *man/computePWMScore.Rd
49132fb45d689e3f3913f6b99f55196e *man/data.Rd
e8874b84f38d8ac5426c9c9b82e8de91 *man/drop-methods.Rd
4b040a7bc7388adc5453ae318e3fbd3b *man/drop.Rd
4b0ec03453ce06540a7a8d9d49883e34 *man/evolve.Rd
dd94ef0963eaa32d01ed775d8a1ab7ca *man/generateStartingPopulation.Rd
d8f4a051a77b33174dfee5a05ae53465 *man/genomicProfiles-class.Rd
ea1c117403b6cd13704f3376b040fefd *man/genomicProfiles.Rd
2354e39d345cf4890f5ff166130e2ba1 *man/genomicProfilesInternal-class.Rd
bfee8d57b3d06ca01f0796712ecc2630 *man/getHighestFitnessSolutions.Rd
fee30ca60e561f888cd3f6ef6f3dc157 *man/getTestingData.Rd
e3c88798f83f7eda478c2b6fa2267204 *man/getTrainingData.Rd
40fdbd2432836125dd452a7e00ddd71a *man/initialize-methods.Rd
8c9df5bb0157fa5ecec7f4f2de1b4594 *man/lambdaPWM-methods.Rd
e394c530d357ca7e0728e8f3ad4b91a8 *man/lambdaPWM.Rd
11cd28062455641fa1570b5df0199d56 *man/lambdaPWM_--methods.Rd
73906ce06fd8d4a2a6b59df9fb260a1b *man/lambdaPWM_.Rd
7e52adf32f44baeead531e1da1b191d1 *man/loci-class.Rd
c3c02e3fa961cb246a49d21b9a242f64 *man/loci-methods.Rd
3561fb059803caf4b1068e61a0f3e694 *man/loci.Rd
257c6f0194b8345cefa522c083a79f92 *man/lociWidth-methods.Rd
cf6e8125980ca119e3e130e563e2a4b1 *man/lociWidth.Rd
43abba379f9b3df791aee91532ffe940 *man/lociWidth_--methods.Rd
16aa6b5de06a9a6f0f9efa3c2b19e0d7 *man/lociWidth_.Rd
dc8563e5901c10cd05e7503ce055e583 *man/maxPWMScore-methods.Rd
8b3d0a8a610288ad9251a1d4429b45d0 *man/maxPWMScore.Rd
b465b9d4e6b8f05af0d47ca4aec11595 *man/maxSignal-methods.Rd
e2f832da0e868c562b0bca15753beb5c *man/maxSignal.Rd
daf7f08045678a5ee82b0fff3f6c2960 *man/maxSignal_--methods.Rd
92029e2203262457f64f34db84588293 *man/maxSignal_-.Rd
f572d3054d8ea49d1dc6c4ebc205cce0 *man/minPWMScore-methods.Rd
840e55f050548c323138ed1f9d35d660 *man/minPWMScore.Rd
141ae9eea57a16fd613beee9d02cf598 *man/naturalLog-methods.Rd
7e3fcdb7a035b722346c9ad821f097df *man/naturalLog.Rd
3123a4d768b3bf5179d3465b8fa677fa *man/naturalLog_--methods.Rd
db75d747231b485da80d4541b6c4ac19 *man/naturalLog_-.Rd
3df2101853115e4094599cad9c86bb75 *man/noOfSites-methods.Rd
1d13bf214f0e84534bf463205991648f *man/noOfSites.Rd
a41c1d2195e2f059e9ef2d0576871e1a *man/noOfSites_--methods.Rd
3e288352a2a27a624710390c8454be65 *man/noOfSites_-.Rd
17d56256694bc0875bf0a35769453850 *man/noiseFilter-methods.Rd
793b5925ae9acf7813d571233fc66a62 *man/noiseFilter.Rd
090de137c599aa14a3478e10fc0f04a1 *man/noiseFilter_--methods.Rd
fcd83f622209fbba37d0922590c9c2c3 *man/noiseFilter_.Rd
3d1d0091eeeb9d1aaf41f18eb6246f1a *man/nos-class.Rd
84ae8d24b2b251b0de5cb8226d368d5e *man/parameterOptions-class.Rd
3ac663b38d93260a2cc28474aa77dd40 *man/parameterOptions.Rd
775db972138d96b3318c1bf2de29e342 *man/ploidy-methods.Rd
d7849b1d9e2a99bb6d5e301aa1592ebb *man/ploidy.Rd
912fe116a423a7f37a9b3c86c5b64938 *man/ploidy_--methods.Rd
39e207dbd48949412f10d530ae6152ad *man/ploidy_-.Rd
9d2e7f65f21ef98b1c2d25d2780c6a9b *man/plotOccupancyProfile.Rd
c1bc94fcc0f65e3d81a4f45e4de01ecc *man/plotOptimalHeatMaps.Rd
4e42db73b48b3a120174c88152dfafee *man/processingChIP.Rd
0e4fd95928ea5742148f9942f4382bdc *man/profileAccuracyEstimate.Rd
6f15c1791ca3cb423d2aa9781716d6e2 *man/profiles-methods.Rd
7e7543e86a87b539f4ffcde88ea89bcf *man/removeBackground-methods.Rd
9bd6f7e7349ca9d4505dd3ff71e906c5 *man/removeBackground.Rd
9a89020a37b5db0139875121c0542449 *man/removeBackground_--methods.Rd
a5f18c6e39ccf5c66ffb2f86d1527637 *man/removeBackground_-.Rd
abfeee98cc4fdb8f7c22083af74b883e *man/scores-methods.Rd
d6ef962381c92fa3ffda63a364a81790 *man/scores.Rd
2cacf06b6e33842d560001b78ff9dfdf *man/searchSites.Rd
3ce4e2c0b2e58e1efc990d66319e8cb4 *man/setChromatinStates.Rd
9681c7a9021b1bdbb7b58ea67c6e555f *man/show-methods.Rd
5fc9450d5046fddf1be0cfeeea4591be *man/singleRun.Rd
6741b6d9a6185483c1d2d36fa3e073d9 *man/splitData.Rd
9112232ba9dce6e36fa7b3c4b772f0a9 *man/stepSize-methods.Rd
0d6632c06e1600fd493274e57a8a3c5d *man/stepSize.Rd
108e0e944c88da281a5ea472b296ae3f *man/stepSize_--methods.Rd
952eb6fa4ab3f6e053fbbe380de247eb *man/stepSize_-.Rd
522ac62894e3bd40f4da3a0bb42ae999 *man/strandRule-methods.Rd
c8b6aebd2c74fa1ac8606725a640aa37 *man/strandRule.Rd
901edd87bf06575368de614407a57fad *man/strandRule_--methods.Rd
2516557d8f19a93f970ac3741850b0ea *man/strandRule_-.Rd
f46081794536d7e855368b481b04b30c *man/whichstrand-methods.Rd
f1eb87122879dd85cccded4891447164 *man/whichstrand.Rd
793d801b7022e266bd811308cb520f9f *man/whichstrand_--methods.Rd
4f0c5c761534dce90250be8dd74e6281 *man/whichstrand_-.Rd
cf99901263cadb5d329813ca8dbb2117 *tests/runTests.R
a0a0bb7d330a5d93dc1b118bbfe5c2d8 *vignettes/ChIPanalyser.Rmd
a0fe48e002e094f9d5687a499d0d008e *vignettes/GA_ChIPanalyser.Rmd
