b49609716cbabcd29fd9dc98039b295d *DESCRIPTION
cd06ca101906c87168e789504fdd80f3 *NAMESPACE
905ed95ddc025882f8a9e09f59e33dff *R/alphabet.R
2615f45e308194af516a3f69510c35df *R/baseDistrs.R
f6ff86dc96cc55c8f09e9b860d53bd6e *R/diffSeqLogo.R
0a4eadb78fc6c17c33267cb665ae8a0f *R/diffSeqLogoSupport.R
9db64bf4c118b6afef235aa3b5dfab88 *R/preconditions.R
9ef2552ab4f4b40ead4231832baf1a85 *R/pwmAlignment.R
0c30cac2f30bb738025da5ef51714402 *R/seqLogo.R
e65acb381814f516286b722afd00adfa *R/stackHeights.R
11db72138f1487d47ab0e712b86056f2 *R/utilities.R
bce16b073e7fef9b62f72b698132a3ff *README.md
e3b824d3df1db4b77dcbfe9c012022e6 *build/vignette.rds
391f8a3899bc796bbed73c5b3212a2d8 *inst/CITATION
fea734b9579c10952c4797b5739e3672 *inst/doc/DiffLogoBasics.R
68c883ea98ff6663d211382a28a0038c *inst/doc/DiffLogoBasics.Rnw
ba3f5612a0c3ad593e7b4d633f58ee00 *inst/doc/DiffLogoBasics.pdf
9e64524098dcc3547b0a5033d37a3984 *inst/extdata/alignments/F-box_bacteria.seq.fa
b638c19a42f513e456205f9f25794d2f *inst/extdata/alignments/F-box_fungi.seq.fa
9c3c87fdf80fefc6cf3d20485aa94743 *inst/extdata/alignments/F-box_metazoa.seq.fa
81c829501e6d19ac9ebe29dc3eecf303 *inst/extdata/alignments/F-box_viridiplantae.seq.fa
45eea31652c9bf73aff2c145ab10ce97 *inst/extdata/alignments/Mad.txt
707dbdd70ccc0cc51590f505e03f6a70 *inst/extdata/alignments/Max.txt
b411ab2abc76e3437ccd6e818df31d54 *inst/extdata/alignments/Myc.txt
d6422185297c2583f4419f467aec0574 *inst/extdata/alignments/calamodulin_1.txt
4d0f44df6595197edd2b21d3549b4e57 *inst/extdata/alignments/calamodulin_2.txt
2cec07f111c114b62e74dc5fda6d5b17 *inst/extdata/alignments/phosphorylation_1.txt
610cceb5049e7cca41221bce75f23d95 *inst/extdata/alignments/phosphorylation_2.txt
c78d0348b409bfaf488df306859666da *inst/extdata/alignments/ubiquitination_1.txt
cdce4193c5fadfe94bc64bd20fd082b5 *inst/extdata/alignments/ubiquitination_2.txt
8c38fdb2ea172dabd1ab4c45ddf5a4cb *inst/extdata/homer/CTCF_SatelliteElement_Zf_CD4.motif
774f4bdd1a44d8c272a63396d7e9456c *inst/extdata/homer/CTCF_Zf_CD4.motif
eaaac1b0e8624dce03d814d29ab7a8ac *inst/extdata/homer/Max.motif
fd5d4c365e7e5de7f31f2adcc8df2a53 *inst/extdata/homer/c-Myc.motif
ccc5a3fef2d1a0e70be046cce43dc22e *inst/extdata/pfm/ctcf_jaspar.pfm
6093b56d5f72163054afddfa7e1013e3 *inst/extdata/pwm/GM12878.pwm
ac0ed6904d023f00b38f953060434399 *inst/extdata/pwm/H1-hESC.pwm
5c049781855e3d08d476eb735e438438 *inst/extdata/pwm/HUVEC.pwm
56e78321b415f4e5f39cb226ddb3915c *inst/extdata/pwm/HeLa-S3.pwm
f340a2bd526bb8cfe484a06f41e0923e *inst/extdata/pwm/HepG2.pwm
a55a478ca869b172f945c7e004de9aba *inst/extdata/pwm/K562.pwm
7256e36aa113e2ef2f25345cdf816682 *inst/extdata/pwm/MCF7.pwm
d7bade5c657d185fc7c4b7e15199183b *inst/extdata/pwm/NHEK.pwm
1e417b7456962e38375fdb5de6c67bb4 *inst/extdata/pwm/ProgFib.pwm
dd127990a6d90197f461bc50290f6009 *man/ASN.Rd
475fd362bc711a279321a84872f7244e *man/Alphabet.Rd
0a089d71619c4326391fc008814f84bc *man/DNA.Rd
83802483b6831f0cc060e97665382f28 *man/FULL_ALPHABET.Rd
6f97324214694c7fb30cd9d835faa27e *man/RNA.Rd
371e1202a0996c8535cf8b27da7b6e0d *man/alignPwmSets.Rd
70f50347ceff798b2487935238ec1616 *man/baseDistributionPwm.Rd
bdab16acfd68f44ed5c22ce92d4daed8 *man/calculatePvalue.Rd
fec382c95b394dc6f7c97c4d5b280cd7 *man/createDiffLogoObject.Rd
658dfe325c804cb898f9de0de344a1f1 *man/diffLogo.Rd
d438ce13511c788d7883b0da06d346b6 *man/diffLogoFromPwm.Rd
6de73a6a762d8c68c181f1a4b76042be *man/diffLogoTable.Rd
2448dee4538b612a75da27dfe482e82b *man/diffLogoTableConfiguration.Rd
e91375dd85747f58182cf67f9f4786f1 *man/differenceOfICs.Rd
2e965f376836aa132a05ab8301910f94 *man/drawDiffLogoTable.Rd
e26c3af5f80b87be83843eff13115bfd *man/enrichDiffLogoObjectWithPvalues.Rd
d202e1f59d75c132af12fb33d49e4111 *man/enrichDiffLogoTableWithPvalues.Rd
ee54cbc23e4e0a79837592c7f8cab682 *man/extendPwmsFromAlignmentVector.Rd
6129adccb1d2cf5e061619b07821f941 *man/getAlphabetFromCharacters.Rd
2511738425662cc2265adfd3d21e61d7 *man/getAlphabetFromSequences.Rd
93c2ce45a6d584fcca59a32f9f447862 *man/getPwmFromAlignment.Rd
0e86880b293e0bec994a154d0079e656 *man/getPwmFromAlignmentFile.Rd
91d090c842eb37b2980a364525512df1 *man/getPwmFromFastaFile.Rd
18c0e4e7db917de6544e6e969fb15c84 *man/getPwmFromFile.Rd
3eab35e9a26cdaf6c93ffa473b023d00 *man/getPwmFromHomerFile.Rd
c91c095ac2ac81feb808fca3f36a882b *man/getPwmFromPfmOrJasparFile.Rd
fd8e382cb225299690c6aebfcb1440c3 *man/getPwmFromPwmFile.Rd
c801d96360c63bd2065dca7f4cd773d1 *man/getSequencesFromAlignmentFile.Rd
8a6c8223c70b7c8f5f6740bb6d08250f *man/getSequencesFromFastaFile.Rd
29511fd0c8c33625751c70d125ff0cc5 *man/informationContent.Rd
3c41c01262b57937c829779b3f689150 *man/localPwmAlignment.Rd
949afc5e8e45616826cfab18155db9d1 *man/lossOfAbsICDifferences.Rd
966c4e41cad6946348a394adac3ef3fa *man/multipleLocalPwmsAlignment.Rd
34382da13f1507a7977c94cf36988b59 *man/normalizePWM.Rd
eb57a02f80a88ec1afc2f4319672ed3a *man/normalizedDifferenceOfProbabilities.Rd
910eaf8c9953ce7079ed37d5f5be0b65 *man/prepareDiffLogoTable.Rd
a62c7d2aa495a797c973d6c72233c284 *man/probabilities.Rd
69bf180d7054676952831cf4d8b2dd31 *man/pwmDivergence.Rd
0861333ee9232497815cd3205af93823 *man/pwmsDistanceMatrix.Rd
1401ba4ee658fb8627595c8afa5a67ea *man/reverseAlignmentVector.Rd
5856b048fa4456ffe44026d6ba09585a *man/seqLogo.Rd
1b0c28ddbc4e5a1810f00cc9def889f1 *man/shannonDivergence.Rd
fa3723412db5ee77d397a28275107b0b *man/sumOfAbsICDifferences.Rd
299c2e5bace0f3106a1c34560c7c19e0 *man/sumOfAbsProbabilityDifferences.Rd
bcbf68a8a53699fbddbda178640f03b2 *man/sumProbabilities.Rd
8b2b18b77a9ba44a8805f900de9dd438 *man/switchDirection.Rd
1c039fc033a78c5646c9a34d9b2c32f2 *man/twoSetsAveragePwmDivergenceFromAlignmentVector.Rd
d41d8cd98f00b204e9800998ecf8427e *tests/testthat.R
797ebffe453f7191c357dff02a473f62 *tests/testthat/test_alignment.R
29885ee265f48db4d8241c3fddaf0501 *tests/testthat/test_baseDistributions.R
4ad40b60c9730dd3f77806ada216e89e *tests/testthat/test_stackHeights.R
cacb8d880b20553a69a8b2ddee990c48 *tests/testthat/test_utilities.R
68c883ea98ff6663d211382a28a0038c *vignettes/DiffLogoBasics.Rnw
