e7529791358e5786849b2a59a61bd4ee *DESCRIPTION
8b13203d21b38f8e40b82a56146221c3 *NAMESPACE
d6424224e3e1862c55673b0861c40aef *NEWS
ed61c2bf19ef6631555d346dcdf71613 *R/background_wrapper.R
3e7770c7ee067e459877a83ccf27fbcd *R/combinatorial_wrapper.R
0d9117186a7379b31487191a229747ab *R/comppoiss_wrapper.R
990307c84eca45992f7a858801af1b6b *R/count_wrapper.R
5ace467528a70ff9c58aeba27c0d2f03 *R/enrichmentTest.R
ba953299db0746ded8683a4a14aa3fb6 *R/forground_wrapper.R
840065de3ab63f0e7865aeddc60f4c94 *R/markovmodel.R
90b9d7b4438d16f89ee91a481946df90 *R/motifcounter-package.R
db63e69ca415518196150daac561581f *R/observed_wrapper.R
74458ecbbc6d494ad4621dc9a97810f0 *R/option.R
4a708c143aad2e359e0cbf8ffefc220f *R/overlap.R
f9d3446be6bd5e34fd5869144446d53c *R/score_wrapper.R
d6fc05811dee17e5b4a9f27becbc01a2 *R/simulate_wrapper.R
587ccf402e3a6b26eaeee83b51c4c587 *R/wrapper.R
0290b050acd7f3b77c05c71da0a14565 *README.md
fbabf336b8c06c1a0f49e9b3c50add7c *build/vignette.rds
dcf427f22f04128570f1d58476f311b4 *inst/CITATION
9b5668bff285adc300c76be2e0699a02 *inst/doc/motifcounter.R
4522999932c71a38ebe74b53da6cb32a *inst/doc/motifcounter.Rmd
51325e252ebcd72c70367aceed621670 *inst/doc/motifcounter.html
50df954ee79d0f5a78eb73d8bc322d4c *inst/extdata/m1.tab
6441842ee60b856a7dbd3e8269175572 *inst/extdata/m12.tab
ab7fc1464e844415056df107769f4b64 *inst/extdata/m2.tab
072c2db184ea9dd62de9a67c747edc44 *inst/extdata/oct4_chipseq.fa
5b38fa6389b08d3a65f21294be7aee07 *inst/extdata/seq.fasta
f142bb690529139fed13c75e0ecbaac4 *inst/extdata/seq1.fasta
9cc226e7e9a2a7797dff257bc31ac5a1 *inst/extdata/seq2.fasta
3b458d2042a7ab6a93442abe29c9edbc *inst/extdata/test.fa
d309d44d1afb8021344ff0e4aeca342a *inst/extdata/test.tab
41a01add41f4e45303e61b6366f07eb9 *inst/extdata/test2.fa
ce47118080dd2341e2af1b366911048c *inst/extdata/x1.tab
0f7fd6131c16f42826fba4895e26b53f *inst/extdata/x21.tab
0cf2f5d8c38b3d48158a42af0589b46c *inst/extdata/x3.tab
85418671c5dc1dc29156d8bed9f1dc85 *inst/extdata/x31.tab
0d596bc3216241c2ef0ac9f67d859305 *inst/extdata/x32.tab
a63c9d9bde5e7d71d5e533284ae38d28 *inst/extdata/x8.tab
2d9be916855aa7ea20d69a7bcc8f741a *man-roxygen/templates.R
e81290c23dcb2bd5d0125126f658002f *man/Background-class.Rd
e65f320a267707abcee5efbf8778cde2 *man/Overlap-class.Rd
7a731382c8b393cf60d19920ccddb909 *man/clumpSizeDist.Rd
a0767ee6c88c9f666b692f1fbceecec6 *man/combinatorialDist.Rd
135563c1421ff1c0c7171dbc51f8a2cf *man/compoundPoissonDist.Rd
8def3f7c668c00dc68120b1c3b8c631c *man/computeClumpStartProb.Rd
9d19caad61a90accbae8428730830a84 *man/generateDNAString.Rd
cf56814e67503ed49728620d9e796a7b *man/generateDNAStringSet.Rd
fb3b6533d0ea8ac151b8bb4ed15f4ac7 *man/getAlpha.Rd
0d1892f90075c5ecfd34760664cc2d2e *man/getBeta.Rd
16e2850b916a96432f8b7675e96c6795 *man/getBeta3p.Rd
23c1af342db02d44f27de7c9ed970860 *man/getBeta5p.Rd
760ba5a0cca089bf9741de8681de8e79 *man/getCounts.Rd
28775d87b95389ec71588f09af33df6a *man/getGamma.Rd
fd99b8491211d2182c2f4052c17a4252 *man/getOrder.Rd
71f6d49b09c82ccab29097b0fa2da1d8 *man/getSinglestranded.Rd
50c24e33d5a6891509b5dfca2428b96f *man/getStation.Rd
2d098c247c53195557679d4db0d0a676 *man/getTrans.Rd
43a6e41d8176a03a6e398cc111058d29 *man/hitStrand.Rd
9cb47151e50022821db61e62ba5bfb6d *man/lenSequences.Rd
efef8aaec1389a2bdacf12a1ba135dcb *man/markovModel.Rd
8c5dea2863e9cb7266ebccbd4e674401 *man/motifAndBackgroundValid.Rd
1137c691d124eacf6cf7c307753a80c7 *man/motifEnrichment.Rd
1c5a3aaea4322ac7d9bed91e090c2841 *man/motifHitProfile.Rd
492fbe00fd2fe20550cd231e76f155e7 *man/motifHits.Rd
b9eb3317e5ba27619eb2d5b8cc87bc99 *man/motifValid.Rd
313dee6ea1c3f6a7f78a411d968efcd3 *man/motifcounter-package.Rd
5d60b4925dc857bc9cda4eb902186b95 *man/motifcounterOptions.Rd
fd79e91b8aa74ad5188636d4fa046c1e *man/normalizeMotif.Rd
bac53d1dea6846f2e758a4680cbdefe6 *man/numMotifHits.Rd
063f06a0e698be32bc32f33032f5f294 *man/probOverlapHit.Rd
5ab72281418fb2b056360b640f828f9d *man/readBackground.Rd
0c8e2b1607a827e6c2230c17f8377946 *man/revcompMotif.Rd
c6c1ea3910df91c7f6514b5895cf2194 *man/scoreDist.Rd
6e1db87b14a90a516acffca8d04cbe59 *man/scoreDistBf.Rd
f11ac7a01de450a1525d1b2ba5ea5292 *man/scoreDistEmpirical.Rd
3308273f319f557dded91d3a0ecb16cb *man/scoreHistogram.Rd
5a81ec28cfd638917b07c73a80e921e5 *man/scoreHistogramSingleSeq.Rd
bf08e1294ea738544bf2edb7353bcdce *man/scoreProfile.Rd
b7eecae2f1283c4f7ae6ad70f5df0110 *man/scoreSequence.Rd
edf247571bd94b7e3120ce0c6b1cfd91 *man/scoreStrand.Rd
cee7f61e9f9f9a93019f0bddbb8bd39f *man/scoreThreshold.Rd
4d137dd2a6bafce6cf334e72ba236756 *man/sigLevel.Rd
d427704af430106b32ca2f318891876a *man/simulateClumpSizeDist.Rd
b46716f38d089b49d7b6d3ade4ac5bf2 *man/simulateNumHitsDist.Rd
b5105375550b25fe7a5273f51b0a9986 *src/Makevars
7343bc2da237f71de5dccc08b527d33a *src/Rbackground.c
7a3023b2d2253dd923300e43f7966091 *src/Rcombinatorial.c
a05e9b61733090f30dbaa4d4871ee346 *src/Rcompoundpoisson.c
24ad44e3dce798cb99dbcdc29b975dd9 *src/Rminmaxscore.c
ecc8d588adb69dc15c80c4517c08df52 *src/Roption.c
489a6f22e6775d6af6a3874487abfb50 *src/Roption.h
4daf436c8d0782b15090c5d364f82605 *src/Roverlap.c
2b036759a98359e52e5eb92feb01dfb3 *src/Rscore1d.c
5fd5a4f5d8097aa2edde1fdfc819abd8 *src/Rsequence.c
96c98b94001211c947eac0a2cdd5630e *src/Rsimulate.c
55e78b26c204ce415c11168774b88bfe *src/background.c
9b4d074f5c4a4a918c0c56149a1be573 *src/background.h
c8ba6d65c5ab2b1f3f6d929e8a57ccc9 *src/combinatorial.c
1ff5a97d1fac2efe94f4f1ec8ab71f68 *src/combinatorial.h
537857ee394fee3688d3b0909bce4710 *src/compoundpoisson.c
b207764790365fe40df732052bce717c *src/compoundpoisson.h
d6715c89893d53fb79f798a18fc676b2 *src/markovchain.c
5f3a6c3e1b0b24506fff77942b916a1f *src/markovchain.h
7acb67b7c7c21247e5b6a67250f24634 *src/markovchain_single.c
c877dc742b92bfe720b4a30d969bf649 *src/matrix.c
17d53ac0786ff68e6c91d5e6e18e7cdc *src/matrix.h
fe4757d54eb672ad8e0abb34ce3f0f12 *src/mdist_register.c
acf06f023c397ea0fc9698b8ec43e595 *src/minmaxscore.c
74ab6eaa097f4a22d1cd8d96de7f4ceb *src/minmaxscore.h
1d43490951b7e252ae71985ab45e06c6 *src/overlap.c
304ae5939115f046ce793347b70f2cfd *src/overlap.h
9b4ea13d3f8d98d10e29384847987331 *src/score1d.c
24cebb637ca8877f426dc3350d3ee7cf *src/score1d.h
2dd98e070289df947d85a770a37d0853 *src/score2d.c
dafcdd98cd172524e0062c413d920a1f *src/score2d.h
bf29cef1db45608bda1c9dc12af139a6 *src/scorefunctions.c
17bd325503011642251dcd3097a43102 *src/scorefunctions.h
a90f57ca686655144b2107644aa90c7d *src/sequence.c
5541e2d1466a7a65b9c6b4486c88ab1b *src/sequence.h
edf36b7c297ef4c9b64910bfd4d0729a *src/simulate.c
5151274df06aedaace4bef8e723de900 *src/simulate.h
ce653fae4afdd96a1d3296b39cdd25ce *tests/testthat.R
cc7358101408dc4e8d10dfffde7c56f6 *tests/testthat/testbackground.R
12a4062b728e042c0b64143461439fd6 *tests/testthat/testcombinatorial.R
e4662e442357105ea48bc34d64cf326f *tests/testthat/testcomppoiss.R
dda05592d074df1eed67f413a831302d *tests/testthat/testcount.R
ae7e22a2106747a41b644c167ff4d818 *tests/testthat/testenrichment.R
c975e61a7e7488500d9a51d1410609c8 *tests/testthat/testmarkov.R
d4e1de26a5191935b2dd4db3f367e419 *tests/testthat/testmotif.R
37d3451581039b61d9ff83690c30ea83 *tests/testthat/testobserved.R
b6e5ab8a70d7fe715d2d814df28076f9 *tests/testthat/testoptions.R
98cd5f64d9377abf47dc21ccbccb7527 *tests/testthat/testoverlap.R
4b1b5f8f08f7c6c3eb977c1203f60163 *tests/testthat/testscore.R
ddd64fc1241e8bcb2d43dd4f3539e258 *tests/testthat/testsimulate.R
b78d1cef3013a2b1df2bf2b1f14ec674 *vignettes/literature.bib
4522999932c71a38ebe74b53da6cb32a *vignettes/motifcounter.Rmd
e4028efb8e28870b033717d317d3b699 *vignettes/motifcounter.css
