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3e8259a91565f4d604812a962b626414 *DESCRIPTION
0462901f3b3d869acb725be92e1b48c0 *NAMESPACE
64ad2e8dcb0dd66dca17b938fa4bbd75 *NEWS
e9eb9ca2dc242eb1b669b0838cc96f38 *R/AllClasses.r
ff09c84ec1168aba874806abaac70510 *R/AllGenerics.r
112f202f81792d00178a7003bb081d38 *R/DB-methods.r
ba890a27f62037eee88bbf563cebce38 *R/DirichletMixture.r
cd4b0ad8f977508058ac0327d7b2e6eb *R/Enrichment.R
5c661e0c9758ff407aab0c9af6a8443d *R/ICM-methods.r
235f957b1acf747690e585ed8aa5803e *R/IO.R
88af4b6e67267340ec3d460826d8e7f1 *R/JASPAR.R
4d7e3a4d72dab149ca3510d37df93df2 *R/Motif-methods.r
8c6498bb8af8209e0d2c8cc151abdaa5 *R/PFM-methods.r
cfd187adaa531cb1f924e414cc243a72 *R/PWM-methods.r
0ef5a7b0ecdc8603cad2ba5510229ea3 *R/PairwiseAlignment-methods.r
83f1c090dff1179778c25c33e7ad204b *R/SiteSet-methods.r
4adc25e35cb303e8580d1082fd345fae *R/TFFM.R
173771ad437bdf1d54fb32a5eb67c759 *R/TFFMseqLogo.R
cd6dd2ac41fa209e6689a8cf244254be *R/Wrappers-methods.r
b448b2779d6219e8198c136f32585250 *R/XMatrix-methods.r
7c747c2881b54c3a17632aa27dfcfa2a *R/XMatrixList-methods.r
0674b53481b619bfb5f75ff292ad3d49 *R/coercion-methods.r
df054a6f22ef50b73d7492ba2a1467f9 *R/show-methods.r
3f5959da13ca0ee03070eb27808dc5f2 *R/util-methods.r
4baaf396b25b92e95626472a7f4cf08f *build/vignette.rds
1e1b6f723c7d6d376d8ed7721eb5bb5a *data/MA0003.2.rda
e74e2c55cac5d2fc0701e328f887dd65 *data/MA0004.1.rda
3c669f5a111229ddda755e0416d699b9 *data/MA0043.rda
1788a8c6de2cc130af0a6a062ca39a57 *data/MA0048.rda
97699eef41ce946dfa635d56abdd413a *inst/CITATION
351cc7b084a4ba1cd01449f5bad5f864 *inst/TFBSToolsBuild/build.r
fb342bcf3426bc27d883c9d8bdd38939 *inst/TFBSToolsBuild/build2.R
3dd4a35e1a3d3556ee32b13147a3d79c *inst/TFBSToolsBuild/timing.R
784c396ea518cdbbe33b869353225b1d *inst/doc/TFBSTools.R
b03d2adeacb192328a8d0cd17a3653f5 *inst/doc/TFBSTools.Rmd
6919c8c59bef7c29841e153a0c7b335d *inst/doc/TFBSTools.html
ddae4a3671aa7c8f585dddeb6442b5ca *inst/extdata/MA0001.1.pfm
ecf5fb280abd62ce8951ce9a07834a76 *inst/extdata/crp0.s
4ec79a4902d3d315ddf7bb1ccc39b8ac *inst/extdata/hg19.danRer7.net.axt
e0958dde6677347b5de25090f9d39b0e *inst/extdata/meme.output
d8d894fa0debb678314c88d2c3c7258a *inst/extdata/pfm_all_example.txt
e79a8420f1e308fb18e0c9feb39f7fa6 *inst/extdata/tffm_detailed.xml
1cd3574f51db5ea1835a8d43768f0b68 *inst/extdata/tffm_first_order.xml
942668b48084fa316e13885bb0c87ce0 *inst/obsolete/PairwiseAlignmentTFBS-class.Rd
c3666fa74ce653ab0926e6fefba16e26 *inst/obsolete/TFBSTools.Rnw
643b486141d031a41695a1e80e4f1c4d *inst/obsolete/matrixAligner.c
32398ffa63fe6dfa953b30c125f8100e *man/IUPAC2Matrix.Rd
f3b9e7c3a61c1cc65ed0bb1d30fcf8a3 *man/MA0004.1.Rd
761b52d6b8d30c936bd96607252a07f6 *man/MotifSet-class.Rd
eebbe2b053013fb3b3617163506bd2ab *man/PFMSimilarity-methods.Rd
3a9efd25f1a4dc8307c6c96e623d7a0d *man/PWMSimilarity-methods.Rd
7ed1dd4d91d24a7b822b95fd692439ba *man/SitePairSet-class.Rd
22619a263967f98f95e2974e8cf73d19 *man/SitePairSetList-class.Rd
a8686d5781f662723d65de55f5772429 *man/SiteSet-class.Rd
9077731e7058d27407ace3e6cf2a5636 *man/SiteSetList-class.Rd
2884c57565c9f92a1c6cc463f521c0de *man/TFBSTools-package.Rd
3b7863a187b92c159b2d95a53dada385 *man/TFFM-class.Rd
163b6127d63334c5c5c2fba39040261a *man/XMatrix-class.Rd
82ca0d1835030352b58e8be2f220ae8b *man/XMatrixList-class.Rd
b9c3493b207ddb38dfaea966a1067799 *man/calConservation-methods.Rd
0bd397b43f91cf64c7dce62c0b4f3e78 *man/deleteMatrixHavingID-methods.Rd
2876eeeb43791382a07f036cf96e641b *man/dmmEM-methods.Rd
c5ada2502fcb638f0b1b44c4dcbb6516 *man/getEmissionProb.Rd
c3d364bdd3f6215698eacce21ea712e8 *man/getMatrixByID-methods.Rd
28cab6f4578c46cc8e84f19201159c5b *man/getMatrixSet-methods.Rd
addc1f07037ba8e4971385e70ac3e8bb *man/getPosProb.Rd
02b4c37230c9124d4708561db34b7aa1 *man/makeFlatFileDir.Rd
8c128372d0cdc245588d0a7b5d13c930 *man/parseMEMEOutput.Rd
0434c8ab6afc4da2f86bbcf84b4569d1 *man/permuteMatrix-methods.Rd
a57b9e8241bca95fc31f77f769189d23 *man/rPWMDmm-methods.Rd
6e25bcab36a3a6a15c8c2ec4a6c06070 *man/readJASPARMatrix.Rd
cc1b9dd9b27c23f084351a26b03f4f53 *man/readXMLTFFM.Rd
4e46eb1950449e471c5a6473755756d3 *man/runMEME-methods.Rd
ba624220d57907de15a2ed52257d47b4 *man/sampleRanges.Rd
0f23143f2418784846e9c39584030fbf *man/searchAln-methods.Rd
9dcd516cb381050ed22687d9aeae8604 *man/searchPairBSgenome-methods.Rd
d4838b6df05c4e1efa9e4e5447f550a2 *man/searchSeq-methods.Rd
d819618b9724e8d2a11fdde0ea5effc4 *man/seqLogo.Rd
c8252944092bffe8f14991513e83a239 *man/shannon.entropy.Rd
c85dc7961f5cc10d2619ad9fba7eaf96 *man/toGRangesList-methods.Rd
84d4ce220e238deb6148019762205731 *man/toICM-methods.Rd
f4885b2fe1c5f240dcb6c12e493f5afc *man/toPWM-methods.Rd
00ee54310dd08428575704cc6743c44d *man/writeGFF3-methods.Rd
fa4e6296c569f92036f19ee769f77cc5 *src/Makevars
25f43987ae60c7124cb6b5d7d9a950ba *src/Makevars.common
044328ee7a5e610a704ca62bcf2fb81a *src/Makevars.win
ad9a76b02c0971f0272c229096fa8266 *src/R_init_TFBSTools.c
5c151d5dbf9724522d3b7b37d13b8c52 *src/TFBSTools.h
ebd06c1cbd5452234187f7ddaa7619fb *src/matrixAlignerDynamic.c
f78b810b76d3d1a620d018f270c7e2e8 *tests/testthat.R
eaeec8ea51a6b2f8e2c7d4a31be5f5b5 *tests/testthat/test_Coercion.R
5ae5272134bc6c6a670347eef4529484 *tests/testthat/test_MEME.R
8a505ef8d50644ff0b6df15d5bfc0beb *tests/testthat/test_PFM.R
ef43ebc0730487df9b529988a7f1e9ff *tests/testthat/test_TFFM.R
71bb55f7cd658358ec87f04a6ffb9a4b *tests/testthat/test_XMatrix-class.R
bb2701e5f00d6082ded855ad2bb10bc3 *tests/testthat/test_searchSeq.R
b03d2adeacb192328a8d0cd17a3653f5 *vignettes/TFBSTools.Rmd
d00f6648c7d0547561d10e290726b21f *vignettes/TFBSTools.bib
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