370f3e859286cd3bbeb88db4216ce08e *DESCRIPTION
4d978cc31cbc2137e645ebf05122623f *NAMESPACE
c594bd38091388b4656b6e0417c59eb7 *NEWS
38907997ba48cd6bcae23dfcb39af9ab *R/AAmotifAlignment.R
11126b5192ff7d85b995f7c5224c56c6 *R/DNAmotifAlignment.R
6cf5d414435516cd1004a01dfde0b26a *R/DNAmotifToRNAmotif.R
c638013d0cb9b3b26deb1fb4a76fdfb9 *R/alignmentByPCC.R
1e1068a44649405496bf405accc1670a *R/browseMotifs.R
dc4cab397c70ee65814912a42aee921a *R/clusterMotifs.R
300ddd83f4dfc649085d04a03fa9b55b *R/getRankedUniqueMotifs.R
d09f44afff1e0deb7af1048763eee5e6 *R/globals.R
8ba07c428fcc1bc8a5c0cd2ea68552be *R/importMatrix.R
f974679b07b24dab680e39b667e3ec86 *R/marker.R
5e21c588a8c4b8a331177a398a327b24 *R/matalign.R
3803a0ac2a95b733213d7e02ec7cfb18 *R/mergeMotifs.R
b46f854a88f7c7dabcf3ca33e477e0cf *R/motifCircos.R
c32d469230a722571d7e739562b735c4 *R/motifCloud.R
deab858a7a483c03e887d97deccd39f8 *R/motifHclust.R
4da251e1cd74973f4097fcb6da56061f *R/motifPiles.R
46ba338546f026ac8928391a301dfe5d *R/motifSignature.R
d9913df90770210f46d88284ac00c12b *R/motifStack-Package.R
18061f8fa3d7058d34b4e212442c5f97 *R/motifStack.R
f2d7e0a8cbd355577d850848434b2940 *R/pcm.R
88c06141f5b574963e3b0791c57f4690 *R/pfm.R
54672a5b3414d9eff952ee0240c1373c *R/plotAffinityLogo.R
3a515f342e7bafa6e5ece4ed908b953a *R/plotMotifLogo.R
5a6d660452e0c6213b8a26a405501364 *R/plotMotifLogoStack.R
1ce164afec7c8c131114af752ce7ceb4 *R/plotMotifLogoStackWithTree.R
decc977857e4c80364af934747f837b1 *R/plotMotifOverMotif.R
a4941c810b593809dc50afd6d8b8b429 *R/plotMotifStackWithPhylog.R
125537c7ea8d5d1f452116004f2b88e1 *R/plotMotifStackWithRadialPhylog.R
3b8427b88121222ca019cb7cafe561cb *R/privateUtilities.R
5b514c3667d80dfd2c36d7df4ad122d4 *R/psam.R
778380cb9e3ec7040b4a6c29e54b3155 *R/pssm.R
fc31ba132c7ce059886efe6ed31b0abb *R/publicUtilities.R
f335c9fff7dde4317d66b1ff348a8b4a *R/reorderUPGMAtree.R
6fe8f78022dd344c9dc95d0f1c9a2b49 *R/signature.R
f101acd59e0ab5c0f09c90e0dfd2b475 *README.md
b951cda1e7ddc21c210ec4a810107ea1 *build/vignette.rds
59e1d2dc2a103216ef167882952bdc0c *inst/CITATION
5e5198d8b55ec9447c581b46cb1318fd *inst/doc/motifStack_HTML.R
32559a3b4f59515ffeb3114c74120695 *inst/doc/motifStack_HTML.Rmd
711e8ea4410f261b3b2fdf4e550815f3 *inst/doc/motifStack_HTML.html
55f25e264915a25cd6a06408a2d05726 *inst/extdata/FoxP_SOLEXA.pcm
edca925d6ca03932e85a81e20c6c0a84 *inst/extdata/MA0002.1.jaspar
38206556aec82e605d865385d157c152 *inst/extdata/PSAM.mxr
49ca2809e633ccf48054d760897a8f6b *inst/extdata/PWM.cisbp
f1917006f018e0afa7c65dbccdd4b91a *inst/extdata/RUNX1.pfm
476254bdfdac69a70d52118f31cdf7d7 *inst/extdata/RUNX1.transfac
b2fbf164bbd6dc7a474228911cf20683 *inst/extdata/bin_SOLEXA.pcm
dfd038758f263ea24573af1ede309d1b *inst/extdata/cap.txt
9bed12e20af7736e7a18f02870ce96e3 *inst/extdata/dna.meme
754b2a418af3f4107db51e7fa8e42697 *inst/extdata/fd64A_SOLEXA.pcm
e24bbad06471338e3713e6a660ce0e0b *inst/extdata/fkh_NAR.pcm
cd9a3b475b43fe9b0be6115776ecb92c *inst/extdata/foxo_SOLEXA.pcm
990397f2b3b01dca6f61d76271ca428a *inst/extdata/momo.txt
de98e2fd2268ff01893dfd15ad7725c4 *inst/extdata/prot.meme
6f616be226dc124d5513bf7f848d3ca6 *inst/extdata/rna.meme
bcfb9eaa52b6e2eaa4b0b291d2de13eb *inst/extdata/slp1_SOLEXA.pcm
f99d218bca1b7bc1f3e6049952383a27 *inst/extdata/slp2.pfm
f1a24bc055a498f934d84e748a76ebe5 *inst/extdata/slp2_SOLEXA.pcm
7f1aed568d2f20b78b3065bed7f894cd *inst/extdata/test.beeml
7bd6a8148a12c067a63284f179b63880 *inst/extdata/transfac.like.test.transfac
b1179879e805cf50b70ed384edfe09ca *inst/htmlwidgets/browseMotifs.js
deb7046766809a4f28af2a53446eb133 *inst/htmlwidgets/browseMotifs.yaml
e58d727c134b6a5d2095e4ca116df4f2 *inst/htmlwidgets/lib/d3-tip/d3-tip.css
a30b5ec9ac85140603906e99744340fc *inst/htmlwidgets/lib/d3-tip/d3-tip.js
dac99cdafcae16ea05f91f4f0070d89d *inst/htmlwidgets/lib/d3/d3.v4.min.js
abf5469ee6202eeb5d4da07e34394269 *inst/htmlwidgets/lib/plotWebLogo/d3-plotWebLogo.css
f0ec32edab9b7bcc5d73844345775d83 *inst/htmlwidgets/lib/plotWebLogo/d3-plotWebLogo.js
0b1f037c74afad49b4a2fcf773cef895 *inst/htmlwidgets/lib/saveSvgAsPng/saveSvgAsPng.js
30a457211b640f4e32eaf24e5d2bc2f3 *inst/unitTests/test_motifStack.R
8eb1c95054b9dcd54beb7240ac34003b *man/AAmotifAlignment.Rd
966f419caa26c6fc11be9ecc6191c9ba *man/DNAmotifAlignment.Rd
06142e62b6918cfa9552bf875dd9fa4f *man/DNAmotifToRNAmotif.Rd
8de91883f79027e8792ac64252586b0a *man/GeomMotif.Rd
3cc84dd1d576604dc2925083c679a692 *man/browseMotifs-shiny.Rd
0aaa5f2cb2afb1082ffe4a22b218a4ba *man/browseMotifs.Rd
b41b4699474ec833d0ddd92e3a61a317 *man/calF.Rd
ab10ad411c5e477a1205849bb3a32892 *man/calI.Rd
6be0fdcdc9f397c23dc9d92fa983f48d *man/clusterMotifs.Rd
3041523e58b66f20ad328cef2951c315 *man/colorset.Rd
aaff7e5dcd762a8ee94cd48682e2a393 *man/compare2profiles.Rd
dee5fa46d33467ff334e3ad69b6e0dd4 *man/compareProfiles.Rd
f5022e78048d06b236687194711cc202 *man/dpGlobal.Rd
3d3dcefc4210e4fccb3e65582d2d109b *man/dpLocal.Rd
4ed06fee6dd079597c9f1516427970f4 *man/geom_motif.Rd
ac797b63572870e8a51dd1295d088c76 *man/getALLRscoreFromCounts.Rd
16bbeeb2e9d5f47091c4f671ef3451f6 *man/getDistance.Rd
b5718de3fc266dc284521fdb566ebd3d *man/getRankedUniqueMotifs.Rd
95580b621a829c200b38f95572592f48 *man/getScore.Rd
ccd4b83f98cde0ccb6c554d42253fc29 *man/highlightCol.Rd
10695e453ce2b87ae33fb18a8ac769f3 *man/importMatrix.Rd
151b0096ad7004f7a6ee0f65cd0c70a0 *man/marker-class.Rd
06e579fd0f76d64903f6eca2cf0c065f *man/matalign.Rd
a1c05102dae146dc188743311e575154 *man/mergeMotifs.Rd
572781f07bbf0d4fff46d30a25c7ac1b *man/motifCircos.Rd
ca0157803bc7112672a2f3117fb4311e *man/motifCloud.Rd
37df5389b85bb3f92e4be9d9ec8d9324 *man/motifGrob.Rd
1160832ac34fd3603ded0ec06934a943 *man/motifHclust.Rd
1851423ef87cd555163b4280119cd186 *man/motifPiles.Rd
fb3e9e5ded47016f8a3d5e28c3bc0249 *man/motifSig-class.Rd
0f8fe265651476b6bd1f7ef1f741fd70 *man/motifSignature.Rd
670322e1b2a09717553835b8cf008290 *man/motifStack-package.Rd
7fe36a898d4a4ab022143d60f8fb29a7 *man/motifStack.Rd
4fbb275379772dcf3221fdbee7281c43 *man/ouNode-class.Rd
262a8438126226b1c1e189c408955097 *man/pcm-class.Rd
3d9a46b69cd10b35dd80d770023ffabe *man/pfm-class.Rd
15abfd6d4092346ffbb913a2b5f80186 *man/pfm2pwm.Rd
2653198f3544ce7b9febe5508e054001 *man/plotAffinityLogo.Rd
c873ed806ba700b60c2038308420a248 *man/plotMotifLogo.Rd
500eef14aefa84b6fc93df77948ca2de *man/plotMotifLogoA.Rd
0ea429913fa396e38eaff136adb50f76 *man/plotMotifLogoStack.Rd
3e25205f10710382136ac21884a5644f *man/plotMotifLogoStackWithTree.Rd
08c3259c7d6e0fa209f8e7b069be2b24 *man/plotMotifOverMotif.Rd
ceb1014c27e50b287ecf918ec38cc141 *man/plotMotifStackWithPhylog.Rd
038331c32cf535481e9d278b57319d66 *man/plotMotifStackWithRadialPhylog.Rd
4dfd251d58a7d108e1d6cf9fb89306c7 *man/plotXaxis.Rd
d92a0d98ab63cd36c0249e985ce306c3 *man/plotYaxis.Rd
214ca22d33ac88a45fbe7d4bef299b5f *man/psam-class.Rd
4cd1af313f384621aa9e8d9fe90f88f7 *man/pssm-class.Rd
e8b2821c80bbbfc6eb45f31b08ce268a *man/readPCM.Rd
102b19d102a17478f90b82c49d88e103 *man/reorderUPGMAtree.Rd
fd482113f824895caf0ea48e2a1eab12 *man/traceBackGlobal.Rd
b6a7ee0a9fb84170d54451380c6528ee *man/traceBackLocal.Rd
7023e2ef0e71e0ccba0c622510ce2dc7 *tests/runTests.R
32559a3b4f59515ffeb3114c74120695 *vignettes/motifStack_HTML.Rmd
2fcaf97a783a254afac21cc1d2e44b8c *vignettes/nature.csl
36db1dbeeba840ee03826e750e750827 *vignettes/ref.bib
