b0ae6339993f86d7819ee54a019091d1 *DESCRIPTION
2cfd6d4006e5d5c1013339357a397beb *NAMESPACE
dd71d75abff2f17c948c102b47476a4c *R/AllDataClasses.R
edb88c5c80798c4f5857812c55776e6e *R/AllGenerics.R
d3532fdc05fc527ef8f55f2dea7cb0fa *R/MotifEnrichmentReport-methods.R
936d71f5364bd9d1f6bb8a48577b8130 *R/MotifEnrichmentResults-methods.R
fc354304fb8cbf542c0e6f5acc8aeb61 *R/PWM-methods.R
67cfd67e59f14b94c1ba601b632f0b1a *R/PWMBackground-methods.R
f461eb1667e8c0cccb3a8969656759ac *R/PWMEnrich-package.R
12790f1b37637c5b9f6c5d6f2185c51c *R/background.R
273f442c24d55ca34aca22399a5b778f *R/clover.R
100d41f203eace824af973f0eed6bbab *R/diff.R
831bcdd44668079a27045425f96547bc *R/misc.R
abff1b4c8e27e5f5212dee6daefcdcbf *R/options.R
873a259fb1cfe6dbd0502b890c53b913 *R/plot.R
035eebaf918a46c18e9214869189c12c *R/pwm.R
16fd1a6b9b0b108446944cf205cc041c *R/readData.R
b4387fb679bead722252de7e282b358d *R/seqLogoSupp.R
381cfcae92b36033ddd929a854ab9ecb *R/similarity.R
7e9f5a8a9ae7e5f11d3347937a1b397a *build/vignette.rds
b7fb900790a740d862746997648dec09 *inst/NEWS
8a00b9d68e1103bb91f1f425cef86f5d *inst/doc/PWMEnrich.R
d9a566a297ac54a9857f2f551dd0773b *inst/doc/PWMEnrich.Rnw
5e8940b9026da1510b68553369031eff *inst/doc/PWMEnrich.pdf
d6239fb6ca5c19a03b48c5ef520c4ff7 *inst/extdata/bg.seq-test.RData
16737864e28ca293c3d43c9dc274e810 *inst/extdata/example.fa
08048d68adc5c8493db6f4350732af86 *inst/extdata/example.transfac
415a8826cfb40c10021953ac725c3f78 *inst/extdata/jaspar-insecta.jaspar
378529a644ccceb87d72f3204dda1d59 *inst/extdata/pfm_vertebrates.txt
d5940ef608cce77504b0927133c8dadb *inst/extdata/stripe2.fa
2e6e376108f87945c08ffde1cd39a097 *inst/extdata/tinman-early-top20.fa
f980cf6e1a56c37da2588b23b5e3525c *inst/tests/test_clover.R
5ac6eb9e4d6cfbd62cf60c4c26bd8dba *inst/tests/test_invalidInput.R
0b26bedee71d0a29f0c38fc32cda75ed *inst/tests/test_motifEnrichment.R
2d850d37342371c6afeb0e055c33c19b *inst/tests/test_similarity.R
f5e5eb593fc6a07c543a53d535fbb466 *man/DNAStringSetToList.Rd
b414c59d78901eaa7258fe7911d076cf *man/MotifEnrichmentReport-class.Rd
c61dc608827c43ea1a236c429a1b4a34 *man/MotifEnrichmentResults-class.Rd
231efcb86ca965c5f98db7d2aeccab32 *man/PFMtoPWM.Rd
0b9a5cc2ffce032140fd249ea1ee9d68 *man/PWM-class.Rd
45a8ac49e1aa085b83d51a450e499b45 *man/PWMCutoffBackground-class.Rd
20efbd34aa7b6801368c08e9dff45b4f *man/PWMEmpiricalBackground-class.Rd
7bc1a93260990e4fedff717089a2fa12 *man/PWMEnrich-package.Rd
aaef6b386bd17c4f5e278701cf79517a *man/PWMGEVBackground-class.Rd
a85cbfd118da9bd768f2aec3cd6e67a0 *man/PWMLognBackground-class.Rd
2125054b45f05022e9e9c0b5ddf10cef *man/PWMUnscaled.Rd
8fc1262f639d970f052990e35b600f66 *man/affinitySequenceSet.Rd
bec66809b722611d5142ad57c598fec6 *man/as.data.frame-MotifEnrichmentReport-method.Rd
d93c6ae99ed3dde36e251e253cc31fbd *man/cloverPvalue1seq.Rd
92f3107ce55cbd5aec5e70585271e39f *man/cloverScore.Rd
8bdf379f35edf3e90a0d107316f93c69 *man/colMedians.Rd
37d5b5922fb7da2b6fff08cd3add52e9 *man/colSds.Rd
9ec7b4dddd9780184c6c5756b7e31b7b *man/concatenateSequences.Rd
9c07930204054fa5b7f0c2019d373583 *man/cutoffZscore.Rd
73f511ea55c968c4d41451c1fb47bab9 *man/cutoffZscoreSequenceSet.Rd
191b2d0df6af557bf04483f26fb4fb45 *man/divideRows.Rd
9541390248dff412005c906eb3ea93c4 *man/dot-inputPFMfromMatrixOrPWM.Rd
9cd5bb5a84d812589778be2a8ecacf1d *man/dot-inputParamMotifs.Rd
b16d15fc7704dcd76114d1d11f11b1e6 *man/dot-inputParamSequences.Rd
cda2602f2508c796e6a1499dd0f000be *man/dot-normalize.bg.seq.Rd
33b0422c20ca65e666f0adedc9d4dc15 *man/dot-normargPfm.Rd
10491fc9e1886682b11123f009f1438f *man/dot-normargPriorParams.Rd
fdf455a2ae7467404d745f1f238e311b *man/empiricalPvalue.Rd
d490a13ceec76d5fc44117835a3f285d *man/empiricalPvalueSequenceSet.Rd
63dc90627ed3ea02f951f52dd4015afb *man/getBackgroundFrequencies.Rd
13cf9496f77d7deb063a56deebafb2fa *man/getPromoters.Rd
b3d8f4c9b6ac88863422ea4336b7345a *man/gevPerSequence.Rd
163177a958391e276e7f4dc7e6bef2bd *man/groupReport-MotifEnrichmentResults-method.Rd
4ff543ca69d20869a4a635aeb5275fbe *man/keepFinite.Rd
66d0126d20f868ddbd373e47a8a1a401 *man/logNormPval.Rd
aa4965d44c5727882f6e9f312f0da5f3 *man/logNormPvalSequenceSet.Rd
e39d9fedf7c060e410467d264ae6a71a *man/makeBackground.Rd
95bf180bd588b6b5f74c339f5341943e *man/makePWMCutoffBackground.Rd
a5aeb10d481454d9b2f89e9b461e9d8f *man/makePWMEmpiricalBackground.Rd
c1833aa62182039f2aeb5d1d5483dd56 *man/makePWMGEVBackground.Rd
e199d73788a8b578b218c286b8b4315a *man/makePWMLognBackground.Rd
d684571267963cffea39ecb9f1c6d62b *man/makePWMPvalCutoffBackground.Rd
e9b5b5e614d69d822677b585fff1a428 *man/makePWMPvalCutoffBackgroundFromSeq.Rd
7c0e623d7fbeb9a90a7ae6eb699b17b3 *man/makePriors.Rd
f90cb5c734bdf59e843c4a6e81b3fd1a *man/makeStartEndPos.Rd
a5bef3f9f85239f704b7b555486be0b1 *man/matrixShuffleZscorePerSequence.Rd
f31b1af4eac718fd796bd407dc6414ae *man/maxAligned.Rd
410c4d440f8584c7e238ccc549abc35b *man/motifDiffEnrichment.Rd
59554e0c47d941541349c9f4dfc1a86d *man/motifEcdf.Rd
56a6d7ceea13243271f958d72ba5536c *man/motifEnrichment.Rd
394496b2643b14b77b56c84493600506 *man/motifIC.Rd
9c334ce2fd8eb0981275e40f26dd0a6c *man/motifPrAUC.Rd
a6ad11e8d4a20e22a2bde39b46fd4131 *man/motifRankingForGroup-MotifEnrichmentResults-method.Rd
940b571e186dd448cac9e57c70fbadeb *man/motifRankingForSequence-MotifEnrichmentResults-method.Rd
dd7888199ae3d21c138f9f53d54de5bf *man/motifRecoveryAUC.Rd
73a77d7a7cae52fe3724b765d597fd90 *man/motifScores.Rd
34002c2a8561d85a451e1523d369220a *man/motifScoresBigMemory.Rd
7d35846b82f5f8e4bbf4d648d9d53ec7 *man/motifSimilarity.Rd
9d1b374d46b6d02447dfb9053c811fe3 *man/operators-MotifEnrichmentReport.Rd
e84ff8f3fc3f3d3e940f350f373441fb *man/operators-MotifEnrichmentResults.Rd
f1b90d092ff3fff40a9123dcc8e7b310 *man/operators-PWM.Rd
245f795874a8c179d9c3e726d983acf3 *man/operators-PWMCutoffBackground.Rd
866e114338a570870b6c0aec70ffd700 *man/operators-PWMEmpiricalBackground.Rd
db393cb36d1afc9c3dac78d7d4440a77 *man/operators-PWMGEVBackground.Rd
25072b1727ee595587a1980f89f5eca6 *man/operators-PWMLognBackground.Rd
653dd9f2c0040b03841b4fc73f06e4a8 *man/plot-MotifEnrichmentReport-missing-method.Rd
19812a0bf17bb0467d67757a5c961e55 *man/plot-PWM-missing-method.Rd
54cc195b9dc0747157e721e3dd0e087b *man/plotMotifScores.Rd
9671f5d12c66dd6d1162a08ec391596b *man/plotMultipleMotifs.Rd
e3846a5c6abc851ec624bf5000ff4ebb *man/plotPFM.Rd
e0c582c557e505c19f375b2bf78c0394 *man/plotTopMotifsGroup-MotifEnrichmentResults-method.Rd
3a3c35a104847e9c31224bad0ed692a6 *man/plotTopMotifsSequence-MotifEnrichmentResults-method.Rd
4d4fb5932d1a46716edc7becc0555ab8 *man/rankingProcessAndReturn.Rd
86e6e0f5ad38e9aab1a48463a7ced300 *man/readJASPAR.Rd
f0b8653336f1dac43e6a4044965cd49c *man/readMotifs.Rd
61d4022d8056865742ddcc86091b607e *man/readTRANSFAC.Rd
286b09f32869d29b13c9d052b5920b63 *man/registerCoresPWMEnrich.Rd
195b4716fd8b78297c525c8a64e5d4ba *man/reverseComplement-PWM-method.Rd
9fcbb02f20a71ce13f6b6933a6f611e9 *man/scanWithPWM.Rd
d7c1edf8a3dc4063aa1832a186d1eb57 *man/seqLogoGrid.Rd
8b50329f2a151b2419d0312afc439e96 *man/sequenceReport-MotifEnrichmentResults-method.Rd
2f64011345a911d08d09a13db47c6b38 *man/show-MotifEnrichmentReport-method.Rd
240aa35a9a0ed946109790029c0acb48 *man/show-MotifEnrichmentResults-method.Rd
61464193d97935a0c6ec93e707045742 *man/show-PWM-method.Rd
3ec9b5bd65bd9f0848bffbcaaa9aa54f *man/show-PWMCutoffBackground-method.Rd
87ed76d82fc51e7cf20fd7846db721f4 *man/show-PWMEmpiricalBackground-method.Rd
01521e83453f135c11fec3894d7248a1 *man/show-PWMGEVBackground-method.Rd
935bf4a76e58f1af702a662090fe65ba *man/show-PWMLognBackground-method.Rd
11477250c96e38d043ca25fd29c0a157 *man/subsetting-PWMCutoffBackground.Rd
f3a5674fe357ba7dc420b357572f8eb1 *man/subsetting-PWMEmpiricalBackground.Rd
5a2716e842b666243284cef0d224d977 *man/subsetting-PWMGEVBackground.Rd
0d6378d3229a7bbc07b8d3710d8c5616 *man/subsetting-PWMLognBackground.Rd
1dcc2c8b9a097c9314d604a18aebeb60 *man/toPWM.Rd
e02763e2bfb47fa863aa66e882e72afb *man/tryAllMotifAlignments.Rd
d3597d4b70e087f85de259ab73b7e774 *man/useBigMemoryPWMEnrich.Rd
19cb7baab092d0a2b6216f1f8ad0769d *tests/test-all.R
d9a566a297ac54a9857f2f551dd0773b *vignettes/PWMEnrich.Rnw
78be77793c7928400de72c3680a9e4de *vignettes/references.bib
