2d7d7be6961723bccc92c9b6446715f1 *DESCRIPTION
cc032f681cc6090675a8dc83eea6c5cd *NAMESPACE
021997d82cbca5c423a3e0c624acd844 *NEWS
b485a21ffb3bb4b484c61229f7e30391 *R/RcppExports.R
18a9086f01a82c07f8a1a769ceec3618 *R/add_multifreq.R
4e25c397c3a3ed44de71844497de66cb *R/compare_motifs.R
ea5af040fb755ad37c8b4eee367f2d92 *R/compare_motifs_lite.R
9065649dee87a329cd0abaae647a014b *R/compare_report.R
26613d0e81fa7bed968726b2578609f3 *R/convert_motifs.R
573e5c902885714ca31cf92436e2b980 *R/convert_type.R
eb549f874379d8869794d8b1c19ceef3 *R/create_motif.R
fdc91aebc6eac8116df4e4dfef6db2fc *R/create_sequences.R
1957851d6bfaa7d5cad41e36736b540f *R/data.R
1be0aba24ca33a513f476b2220be89fa *R/dedup_hits.R
cbdfa712fae8dfdaa38b782f8ffd9da5 *R/enrich_motifs.R
3ce247f931b2d97e823453c76b258da3 *R/enrich_motifs_lite.R
114d5d31d6437ce765a9611d3721abff *R/filter_motifs.R
798f5efbdf95847a62115350e7912137 *R/geom_motif.R
f049d8811325d1340edd6e7652a19160 *R/get_bkg.R
28bc1554539cec9b212def07c2f13843 *R/implant_motifs.R
dc828448035d6280814673a76ce4298c *R/make_DBscores.R
0bcb4b62e9052b20ed63a7caf7d50b94 *R/match_bkg.R
819205684a1a5f48c25e9e24fd402737 *R/merge_motifs.R
cb3f802c6afbf1cb64d03b52a4682542 *R/merge_motifs_lite.R
94be50d5e3f9b7227c2934001460e61a *R/merge_similar.R
0afaf39dd68b63130b022d7a89444d79 *R/merge_similar_lite.R
37529edb8fe057fb94d64552b037520f *R/motif_coocc.R
6bafecd6f04645aeea32668d7861cae2 *R/motif_finder.R
84014f5e7d33b9cc4309f59e44b4a92e *R/motif_peaks.R
cf7ce1ff717ccc9c8be1a4b20ed91c2c *R/motif_proximity.R
6b2aae684d51f0a76f84a069f4e24afc *R/motif_pvalue.R
92f55c7d0090a7152f0a037e3b22fffa *R/motif_rc.R
9f79593b5ee3e676380d93849ee6bfc6 *R/motif_tree.R
41da7682c1536a9ae62062aa865a1478 *R/motif_tree_lite.R
073effe1ca360ee8ab65672d6d0818e7 *R/read_cisbp.R
f985d5ec02d1d4aa9720b904b2daa575 *R/read_homer.R
4e39825502eaae4ab1a0f21716179a0b *R/read_jaspar.R
cd66b6f74d15211f977be49f44b75ea5 *R/read_matrix.R
5b39c49392a8c80311925edc7ea3603a *R/read_meme.R
d41a086c981caa5c8179d39eb28dfe30 *R/read_motifs.R
4c0609a684ba5952baabbc9cb82f004e *R/read_transfac.R
351fccb5f76c22d3cf5d9302dea25909 *R/read_uniprobe.R
c50025feb7a7c20f35d3281d8cc8aa59 *R/run_meme.R
70dbd5b4299658b447e0fbaa22863c78 *R/sample_sites.R
2774dee6a6afd7849e68a293515597d8 *R/scan_sequences.R
2100535de03c253d440a1c3248bc9ba0 *R/scan_sequences_lite.R
e84803c565680aac1d71263bafd6dedb *R/sequence_complexity.R
85b6627ee29593d97e5999223a9e5629 *R/shuffle_motifs.R
0b165b74d3f0910bb979c2ca297e20b2 *R/shuffle_sequences.R
c2a48d26fbec274b3fefc24855e95584 *R/switch_alph.R
4cf67c9ccfbd3604b7dd378a7477fcc8 *R/trim_cwm.R
99925312d1cc55d4dae52034c4d30eef *R/trim_motifs.R
342e27f46f7685c8a126df4a496f142c *R/universalmotif-class.R
07b2599e0b59bcf5b836cb446a6a9e8e *R/universalmotif-methods.R
463236c416d2a21e4695f74b52379594 *R/universalmotif.R
90c9fc622e2f8fdd520a528235b01cdb *R/universalmotif_df.R
9ad80af2e8c86a17e35440cf1a3c7a3a *R/utils-internal.R
16a3e524bf027c43951e5c47ddada083 *R/utils-motif.R
a679aa1a489f9ae0ca6316e1efb1e591 *R/utils-sequence.R
4c7e3574b40f8e43aabf4a73429dd067 *R/view_logo.R
249f460d366f52c061dd356d5b96d9d3 *R/view_motifs.R
0cd3241672e2ca51c56979cddc1a7fba *R/view_motifs_lite.R
f5765202ed91269f380f785a5e041e38 *R/write_homer.R
26515daee6ff0c6e4805635b49c048fc *R/write_jaspar.R
84d2181a245e99688ec01ac72510c65d *R/write_matrix.R
64e9793e919cd24194dbb5d1eae8633d *R/write_meme.R
8ca697b240ac45d9068363d1c3c0adb4 *R/write_motifs.R
9b0360ea98f8d334460a7d7aab90a306 *R/write_transfac.R
5f8c5e1a940f535645e41f3988ba5e08 *R/zzz.R
4e79571bf3ddde88711d430e3dc3bc3d *README.md
21c9401b8c07f38d762ade4612fc4ffe *build/partial.rdb
7171ffb6416be7a1698434933de9b59b *build/vignette.rds
0fedcef806ff67bd21def474f8c0f686 *data/ArabidopsisMotif.rda
d0b4e05425d4ee6535314c72c6f96324 *data/ArabidopsisPromoters.rda
589c8820070ea73cc9b496f3cb2cf798 *data/JASPAR2018_CORE_DBSCORES.rda
5c13cfbc05b51a3f49fa10a9e5cee450 *data/examplemotif.rda
53beda63dcdcce418f110b05e89da6e4 *data/examplemotif2.rda
e53c0bdf1f9aef71c4fed935c474b7a0 *data/fontDFroboto.rda
9acec33be2e55c066738c898f88a9dd8 *inst/CITATION
96eaba4a0215f8ee517c06e1eeb5386e *inst/doc/ChIPseqWorkflow.R
a613f1a8d1c38b7d08cea6a02f8d1930 *inst/doc/ChIPseqWorkflow.Rmd
507a0aaeed7c0bae7383fed8b55d65a0 *inst/doc/ChIPseqWorkflow.pdf
37a263dd37485d2e735408cfb7275e12 *inst/doc/Introduction.R
82422a51052edae478fded003bfede2c *inst/doc/Introduction.Rmd
0a255252a0d4a2646981e27c6b00c46c *inst/doc/Introduction.pdf
34211350e9ca1468223a2c1ac0d0a6fe *inst/doc/IntroductionToSequenceMotifs.R
251ffb10daddfff30c7ddf4a6110abf6 *inst/doc/IntroductionToSequenceMotifs.Rmd
ad93277e37a777e5347b5cef2c8e08b8 *inst/doc/IntroductionToSequenceMotifs.pdf
5bddafc969165be6f8211c8ce5b52c34 *inst/doc/MotifComparisonAndPvalues.R
1cdfe7a4ef7d2185adeac792dd47159b *inst/doc/MotifComparisonAndPvalues.Rmd
2fdb311164d252f96da575dfb016bdbd *inst/doc/MotifComparisonAndPvalues.pdf
0bec5d4f7c71b6f9089e79d919ac88c5 *inst/doc/MotifDatabaseCuration.R
8fc4f88b0452fa617ef846dc8039c729 *inst/doc/MotifDatabaseCuration.Rmd
6b282b7019c85ec6657e4df0a1027331 *inst/doc/MotifDatabaseCuration.pdf
6f810d345037f5c2c1568393f2156ed8 *inst/doc/MotifManipulation.R
0a688dd0c9b8d3519fea54303624f480 *inst/doc/MotifManipulation.Rmd
57e3eab085244aa68af2bb0f7943bdc7 *inst/doc/MotifManipulation.pdf
cfe32aca5106381302b92d9b117443d1 *inst/doc/SequenceSearches.R
3a04db41a17bd29181997b04d868767d *inst/doc/SequenceSearches.Rmd
8087f2c880a413cb90b1ff6678c79709 *inst/doc/SequenceSearches.pdf
5ed00b008fcb103ea143cc171630d0f7 *inst/extdata/VAL1-GFP_val1_calledPeaks.bed
a2b30de61d36bf4757f9bf99489d0214 *inst/extdata/cisbp.txt
5a12ccc2085c2392d7551fee171455c5 *inst/extdata/dreme.txt
4cecec99fe4ab206f13975d6093eb915 *inst/extdata/hocomoco.txt
923edc3048e0ff7f261e9214ca0fafcb *inst/extdata/homer.txt
e6b0f8b479b936f984ef01243e8f5df5 *inst/extdata/jaspar.txt
6548da897ef43bec4d49c322bd79a091 *inst/extdata/meme_custom_alph.txt
39207ee07de83b383f8521d916c75774 *inst/extdata/meme_full.txt
d11f29343e052cc45f7ecd0583068aa0 *inst/extdata/meme_minimal.txt
582aba832d47b73437c26bb3d404b33e *inst/extdata/sites.txt
a3928e8c4de05761f0bf112a7af420b8 *inst/extdata/transfac.txt
bbb960134e63f044692949eb649459ca *inst/extdata/uniprobe_full.txt
3e0c0a6e00821a9e857ef83ae18d27e8 *inst/extdata/uniprobe_minimal.txt
4ecf8e379448fe83328c641cdbfee51c *inst/extdata/universalmotif.txt
eeac9d4bf34a84d31d6d5079b86bf5cc *inst/figures/cwm.png
5e29532dd526357344874a3bc9b82de0 *inst/figures/example1.png
4e60f3c14bb1d00b9eaca1667aed0f99 *inst/figures/example2.png
6c12bc59792884fd3bf98e5705a8c6ce *man/ArabidopsisMotif.Rd
e668daf86a459c5f13e41f35d73e2a90 *man/ArabidopsisPromoters.Rd
a8fa910492c236b5c9ef28aa95756c89 *man/JASPAR2018_CORE_DBSCORES.Rd
67579ec2ccd27f0427b2b4d55d18ab83 *man/add_multifreq.Rd
335197cbb7aeb138a3f5fc98f730eeb8 *man/compare_motifs.Rd
7910784181c53c8a28829b2ea5b850c9 *man/compare_motifs_lite.Rd
7be78345e185f0759580d47efa940cb3 *man/convert_motifs.Rd
ec71dfa5803a966591748da7708436c9 *man/convert_type.Rd
8257c3207ea5fc8d6f32df458bd62a5e *man/create_motif.Rd
5d63bd5c46e882f65e0b3267b47563a6 *man/create_sequences.Rd
74a4c241fc0dcfb200a2a435813ad25f *man/dedup_hits.Rd
93e28636ec9d280ab3e021bc0e20a630 *man/enrich_motifs.Rd
bcffb9ae660f1bc1c21e6109e5f56513 *man/enrich_motifs_lite.Rd
0a87580a52fd4479423717b381f6c241 *man/examplemotif.Rd
3f236740ad5329d3cf73b6dc3d3a301e *man/examplemotif2.Rd
3f58fb20d74e6f25cc9703e47b1455e9 *man/filter_motifs.Rd
de727e977f7c6a3908c00eafab9c2c73 *man/fontDFroboto.Rd
f61231e6df650b493feb4a6b560f8020 *man/geom_motif.Rd
204acaf92b694de2be6b085f0850d448 *man/get_bkg.Rd
373c701cc56f3e41fe1084d14ecc70bc *man/implant_motifs.Rd
b9ef9c02a514d38287e2cebd6b8e8797 *man/make_DBscores.Rd
12e9c36f515198688c54a2f7bc895ff5 *man/match_bkg.Rd
65c4f23dc5a6c1b6c5517e54b776d843 *man/merge_motifs.Rd
be5d21efbaf32248660f42dd58458209 *man/merge_motifs_lite.Rd
fea140514bd5800fdcfa06a6265f3308 *man/merge_similar.Rd
6f37732d4e2a4781bdc78b059e656bde *man/merge_similar_lite.Rd
ef7086374a5c3fc7184e5c6f95397140 *man/motif_coocc.Rd
6396f66b4761827c006cd6d0bb5c1899 *man/motif_finder.Rd
b61a6f5067a1ae1b308399899efa0e69 *man/motif_peaks.Rd
c65163ff01a4f9c2dea9cabcb3e84b17 *man/motif_proximity.Rd
4eb662796637ada34d4577702c66fff9 *man/motif_pvalue.Rd
79777a15400baff69ee19314705f5718 *man/motif_rc.Rd
b6f5bf0f3229982e65d6c18303df066c *man/motif_tree.Rd
db793e539fac1e39bcca05e073ed7ff4 *man/motif_tree_lite.Rd
a73c4b4b83dd64adf5bf3c86944af8be *man/plot_match_bkg.Rd
6dad0312c5be0ac56288e78e0ad761f2 *man/plot_motif_peaks.Rd
fc32cda4a2f02e72997d435740a3dc97 *man/plot_motif_proximity.Rd
a54c467e284b2e0f76e9479179f8f72b *man/read_cisbp.Rd
714811310d47ec85c5f4a517a2b2e74a *man/read_homer.Rd
e4b42659c90d327a34b1fd76d938751c *man/read_jaspar.Rd
b657d7b450b5bf7778cd70b85a0ab6b5 *man/read_matrix.Rd
d2d497a085ed30ed299b4e208d5a70d8 *man/read_meme.Rd
4d6c99a9b12b03fbea7f4bddd28ca7a8 *man/read_motifs.Rd
29802edfcc42a5aa60f96df46503d3ff *man/read_transfac.Rd
896e231cf07d50e7bee3c584c15db41c *man/read_uniprobe.Rd
057517db19acb136bbc5bfcb7cb0dc37 *man/reexports.Rd
f73948f1c7e3bf256eafacb48ca2d138 *man/run_meme.Rd
50301a470dbcd68d8b34458d13bb91f8 *man/sample_sites.Rd
c7200c92586b29bec6ba3eb660b621df *man/scan_sequences.Rd
196647f492103185583fbe245543c4b7 *man/scan_sequences_lite.Rd
efda7a6ccc928b4deaaba5cd28c630d2 *man/sequence_complexity.Rd
a1aa61b5bee72692fcfad63fb13af4db *man/shuffle_motifs.Rd
d1db617486c4226d4189a602925063f1 *man/shuffle_sequences.Rd
233cb675e1bee1817ca9c494dea2779e *man/switch_alph.Rd
4b948592cbd8c764af474a830663613c *man/tidy-motifs.Rd
9391156ba82b4b1b6571f90cf7b60317 *man/trim_cwm.Rd
815dbc13a49a2a5f295d5cec6687c6d5 *man/trim_motifs.Rd
de30d2a6f86b646cbe2403a65e24550c *man/universalmotif-class.Rd
c1a529ab8190f494856fbfbafefe5c02 *man/universalmotif-pkg.Rd
ab83eead449ae17e2c7f418ab2b83271 *man/utilities.Rd
32070f1cd6474491f05843524bd92a29 *man/utils-motif.Rd
51184ae51f9811b138cd38e78314f970 *man/utils-sequence.Rd
e8849c59ea323f2bd38904cfcc42e211 *man/view_logo.Rd
84a611420a1fb9a7af19d39a0e7cd35e *man/view_motifs.Rd
6e137d21109bd78df898570d15eaef44 *man/view_motifs_lite.Rd
b9052741817cf9b519d74b0131734b25 *man/write_homer.Rd
bbfb7c1435149f5b1fd6d97364a6bc58 *man/write_jaspar.Rd
a2feb7973c2013a176ae413d69dbc88d *man/write_matrix.Rd
024415f6914a8c55eaf21a64bc0fe9ac *man/write_meme.Rd
0874f67036cd432dc48ea5e882f32ba0 *man/write_motifs.Rd
9a1d4933f624b72757d2b903e0f15e13 *man/write_transfac.Rd
fb443cf09c6f6b98bb87c8e02b44213c *src/Makevars
f5fd36f06a4578c3507e7474eede87c3 *src/Makevars.win
ec88a6854e794a614ac4ba522432a8f1 *src/RcppExports.cpp
319578c165e447cbc05fbc04810a4b9e *src/add_multifreq.cpp
8e7d389356abfbcb6e94fe2bad3cc5c8 *src/calc_complexity.cpp
6847f8febbb331883f8bea5b4022d36e *src/compare_motifs.cpp
5b9688a6c8d26987fa1bcec70b71a959 *src/compare_motifs_lite.cpp
46e9f91ae73e8770c34109cb85943bd5 *src/dedup_hits.cpp
9638436171675721a8c0fa1af487d033 *src/get_bkg.cpp
48b24e7529108a3bd4db27b513313f03 *src/motif_finder.cpp
4a9d06de4174983f986f88d191042d01 *src/motif_pvalue.cpp
92bf56fb4526f6fd10691c200f314ae8 *src/scan_sequences.cpp
ca3c69f88d18e2b33c39881d754fd9c6 *src/score-grid.h
32fc200d31023316ab403381f066a520 *src/shuffle_sequences.cpp
c6de1c4da895c968dce2b9817a8b8894 *src/shuffle_sequences.h
738e14bf6eaf4559256af7f0819b1dfa *src/trim_motifs.cpp
6d6b5bb5965f928e279c335f79f6fd82 *src/types.h
7fdf63b7d5cb14d71ac4d7f5ff208639 *src/universalmotif-class.cpp
d50b63b5349f69d3be276cb0fde7b037 *src/utils-exported.cpp
8b60104e5ed091632c574104c37424cf *src/utils-exported.h
7b9cb53c90ca67a12a318df7e7577f8c *src/utils-internal.cpp
6eeb9b95d9d3ebf4b35b819b08b9cfe0 *src/utils-internal.h
0622a97a2aaa3c342f09636052c2d7f5 *tests/spelling.R
4e3a5a94e661dd25f836adb5f425c1ff *tests/testthat.R
92542ec0951ab0a785714ffb9a359a0b *tests/testthat/test_add_multifreq.R
268300c373cede8d19ec6af19a432298 *tests/testthat/test_background_contract.R
ccea21e547a29a2043ab8953606252d7 *tests/testthat/test_compare_motifs.R
c5b256bd6d4f15a1907cd73f900fe146 *tests/testthat/test_compare_motifs_lite.R
eafc5f3dfcbcf5602ca0bf8584f515f2 *tests/testthat/test_compare_report.R
49a78e41eebc9a9c978208df297e7ee4 *tests/testthat/test_convert_motifs.R
8df244a23fc18c59a1072259331e8184 *tests/testthat/test_convert_type.R
4116b7254663fba3ea5f8b37e7b1ae6f *tests/testthat/test_create_motif.R
3aaa2ce498869ce558c9daf601bef9d5 *tests/testthat/test_create_sequences.R
f2e10176dc8895586ca7aa1d960938f9 *tests/testthat/test_cwm.R
db2118541c0c317007531d633cf14753 *tests/testthat/test_dedup_hits.R
64896fc319a24c93ff5e0fcdb358fcb4 *tests/testthat/test_enrich_motifs.R
ce839dfd7b54d1e93a1f577bcdeab221 *tests/testthat/test_enrich_motifs_lite.R
7b5d717012da9d5f1a8db169197ff682 *tests/testthat/test_filter_motifs.R
93733975f75985bbab47bb39d56ece60 *tests/testthat/test_geom_motif.R
4ddafddbcb635d0272e74ef9593ed698 *tests/testthat/test_get_bkg.R
1f9678a842aa284cb39852e14712258f *tests/testthat/test_implant_motifs.R
ac7e950bbd2b90e7d2ba1096c1e8ced2 *tests/testthat/test_match_bkg.R
8ced9937427a926bc97e409fb5ac5c3a *tests/testthat/test_merge_motifs.R
a7d3356d18d4b1c594df03c50ce233d0 *tests/testthat/test_merge_motifs_lite.R
15899db7690392e091f9d381defa20c6 *tests/testthat/test_merge_similar.R
d1b777dff7a705e0ba3449c574113b68 *tests/testthat/test_merge_similar_lite.R
f525313a52c5a97d157d6fea1f8030f5 *tests/testthat/test_metadata_boundaries.R
274dd89bd9aa94d387d1c702a884d770 *tests/testthat/test_motif_coocc.R
9a630ed1d0a628ca40dff1d43a4f05dc *tests/testthat/test_motif_finder.R
51c56a65ddbf14a120a9cf64e87d06e3 *tests/testthat/test_motif_peaks.R
83dea2b4ba6f8e815affaf5c666e2eb2 *tests/testthat/test_motif_proximity.R
f6e3b838f86259c1308cd1d6c6baef7c *tests/testthat/test_motif_pvalue.R
1493fb498fdf70102250c57ed7bb8a38 *tests/testthat/test_motif_rc.R
64e0522123cfd7375542a5368d28f588 *tests/testthat/test_motif_score.R
15b683c9a7be9619105cce139275d747 *tests/testthat/test_motif_tree.R
9c8a5b0feeac8d8d5e7fbec5ad097390 *tests/testthat/test_motif_tree_lite.R
4a2f1fbf2dc3cfdb3365fb64a3ae8788 *tests/testthat/test_read_motifs.R
8379525c46c244994cfd57acb62f4323 *tests/testthat/test_run_meme.R
eb60e04da498e488248181b3286cdc4b *tests/testthat/test_sample_sites.R
a8064944ab2fa77d99a05fcc18aa3581 *tests/testthat/test_scan_sequences.R
1e91c9e8734a3669ccebc9393894ae93 *tests/testthat/test_scan_sequences_lite.R
8c2ac567ae5ebd8e34ce9542576bf693 *tests/testthat/test_sequence_complexity.R
f558f28efc042c09161f81aa090b6461 *tests/testthat/test_shuffle_motifs.R
bc83ed6ba73efa3cb373c9be42ec333b *tests/testthat/test_shuffle_sequences.R
8ee1a4ba8a9f46731c3df771f2716561 *tests/testthat/test_switch_alph.R
dfacbc94a45a9c06557ab210eb285753 *tests/testthat/test_threshold_contract.R
b3fddd0c4368d42dd87c9065a342dff7 *tests/testthat/test_trim_cwm.R
f4b6b7ab2cd578a41026c08bce4061a7 *tests/testthat/test_trim_motifs.R
61e93ea17ee93c268392c4018d37cda2 *tests/testthat/test_universalmotif-methods.R
253405b99e0362939500661648c8ca20 *tests/testthat/test_universalmotif_df.R
e7b72b62686b48733a9c20dbf95679d0 *tests/testthat/test_utils-motif.R
dec56e7c10d2d611b31cd9816e049fd4 *tests/testthat/test_utils.R
a411b678b8d57506f1fb8409d51a149f *tests/testthat/test_view_logo.R
4595a4afbdf4bbc23faefaa5cbd668be *tests/testthat/test_view_motifs.R
fd3db16b91509a0fbd5c443261ec449d *tests/testthat/test_view_motifs_lite.R
4e141c5fa90fd51bb014949706569b8b *tests/testthat/test_write_motifs.R
a613f1a8d1c38b7d08cea6a02f8d1930 *vignettes/ChIPseqWorkflow.Rmd
82422a51052edae478fded003bfede2c *vignettes/Introduction.Rmd
251ffb10daddfff30c7ddf4a6110abf6 *vignettes/IntroductionToSequenceMotifs.Rmd
1cdfe7a4ef7d2185adeac792dd47159b *vignettes/MotifComparisonAndPvalues.Rmd
8fc4f88b0452fa617ef846dc8039c729 *vignettes/MotifDatabaseCuration.Rmd
0a688dd0c9b8d3519fea54303624f480 *vignettes/MotifManipulation.Rmd
3a04db41a17bd29181997b04d868767d *vignettes/SequenceSearches.Rmd
9d4b2c675eeeb84fb14ceb0a775aa34a *vignettes/universalmotif.bib
