ad751350a9be61117e054d0205345c02 *DESCRIPTION
8b73c38672c485cb5b4018e104ea3cca *LICENSE
8834c35d805af01432d1911dfa740e47 *NAMESPACE
6b4a11508367d0fbbc6df5137038efea *NEWS
97ca8edd8e618890c609b60e9a781d5b *R/AllClasses.R
a899003a230097ec2303a8e393539a82 *R/RcppExports.R
1beca8e66f614a8a7e58623245a91b3e *R/combine-p-values.R
a6a6a4b130cafa2d67e881d7eb2aed71 *R/data.R
abc305ac883cb60c6f9733c5c0c5bd85 *R/k-mer-based.R
c6cc13a1f9037b31f498b3dd1ce69be7 *R/main.R
ca1f2ee549b35fefa4b28fa8934e8ee6 *R/matrix-based.R
422a597124fb7f8b5fa635d61ba68faa *R/methods-RBPMotif.R
cd3f4e71224d173b0ad7cccb040121d2 *R/methods-SpectrumScore.R
3e37aa86e496d493eea5c1fa9af8e59c *R/misc.R
136ded75429a04cc7965d550369090ff *R/spectrum.R
68c6853eb507741b28d71b20847a97d8 *R/transite-package.R
2da2c7fa508a52f52d736d3d5744fd27 *R/zzz.R
e09e0e3cef115e53873b10d9cfcf7d9c *README.md
2ff554deb2b834646174b35fb9d45893 *build/vignette.rds
e3d3d18990f729050219d1961ad37a12 *data/ge.rda
760d09f199856036dfcec31488aaebd9 *data/kmers_enrichment.rda
7c884a4921235d14642236f55d4d5ff4 *data/motifs.rda
7ea7766ca30c06d5904f0978b14279e0 *data/toy_motif_matrix.rda
562ac3646dd6edaa67104458f3eea698 *inst/CITATION
cfdd9930c7c6d5215605168a72a8505b *inst/doc/spma.R
839f2406ec6bbcc4f3109ce3d8b8ba65 *inst/doc/spma.Rmd
1b5fd369760aef78aae0ffb10e16777e *inst/doc/spma.html
415ccb48a29a2b65f11f84e40a58ab89 *man/RBPMotif-class.Rd
4134a97f9ddf05c5878bfa6d92198584 *man/SpectrumScore-class.Rd
e6882177382b5d4e02b7884917e988cb *man/calculate_kmer_enrichment.Rd
54c62ec8b0a113899892bccc781082fb *man/calculate_local_consistency.Rd
aa832dc547cecd954c1406b3c5bb3fdd *man/calculate_motif_enrichment.Rd
ee23482148f5920f2f0ccb7f7b0ad17e *man/calculate_transcript_mc.Rd
e031ea797480fe458a3c3f0928b9b942 *man/check_kmers.Rd
a828670a5f67120468ee051df836222c *man/classify_spectrum.Rd
634bd1cde6297703461d174ac657ac6c *man/compute_kmer_enrichment.Rd
50b0f7dea1e183b514aa87c40c949417 *man/count_homopolymer_corrected_kmers.Rd
fae1d5cf5ae6611bab8dc1181fb2d477 *man/create_kmer_motif.Rd
0e50acf6867e106cf793eb26892ed8a9 *man/create_kmer_origin_list.Rd
3f0e0b10a15bd16a4faa702fa5c8c23d *man/create_matrix_motif.Rd
2b6f4d3640ae38eb24a00a327f610ade *man/draw_volcano_plot.Rd
2a89d5d08fdccb5417ed7e863555191a *man/estimate_significance.Rd
f93726ad90996b1180a6f912ea8502c0 *man/estimate_significance_core.Rd
27ba6b670a0b81e18b878f6a93ad99f0 *man/ge.Rd
8f4670ffbbe64c874634f5eb5b7db205 *man/generate_iupac_by_kmers.Rd
9f4bb242b8514ce8c9627f78e2eeb4b1 *man/generate_iupac_by_matrix.Rd
43fca7613826ed5a8597c1910e2bfe19 *man/generate_kmers.Rd
1331bd8579d5c515afff04d1c8917629 *man/generate_kmers_from_iupac.Rd
7b6c185c8f17d60a6cb7f4d77792e656 *man/generate_permuted_enrichments.Rd
d7d6f5e3b971daf03cf17f21dc3d0ea9 *man/geometric_mean.Rd
cead5a07fc87a539debd652e9f5763bc *man/get_motif_by_id.Rd
178cfd3f64f909bafde921ddf86a41d3 *man/get_motif_by_rbp.Rd
114cbd5ca084cd3a5c4ca50a4e6015ad *man/get_motifs.Rd
b31e5491463da2ebc4a8b26571bddde6 *man/get_motifs_meta_info.Rd
fcd44c5f6638c302edb3e482d3e57de6 *man/get_ppm.Rd
708341785994970fd5417762037303c4 *man/init_iupac_lookup_table.Rd
a01a8cbefa3156ce6a7520fb8d404bd8 *man/kmers_enrichment.Rd
c4c184e0712e2cc01977ab2cdfb01f4e *man/motifs.Rd
39c95c4353ff99f880ea7058c9fa2fb1 *man/p_combine.Rd
e891923590568531fac30f1c69280ddd *man/run_kmer_spma.Rd
fe57ee8e1839a5742a61b0e1b28fe177 *man/run_kmer_tsma.Rd
6a215ac3087cb79d94c68ae1977acf68 *man/run_matrix_spma.Rd
414ab327b2fe5c0d1cd740ad00992401 *man/run_matrix_tsma.Rd
85f1f6a7d39e10e488f8856549f70b64 *man/score_sequences.Rd
667aa8fb55faa24fb30b3b89bb069746 *man/score_spectrum.Rd
9bf3866c3422215ebb3a653eaa6d0dc3 *man/score_transcripts.Rd
6d9d026e077ffbc7d2067ee2c68bfbc3 *man/score_transcripts_single_motif.Rd
d89f6ac18680ae00251bccb57473142e *man/set_motifs.Rd
99cecf4d0795efbe13d655e519c6c160 *man/subdivide_data.Rd
69c03cad218795f5bd175f4aa90e4d21 *man/toy_motif_matrix.Rd
c27e7e8f5583cf2dcf69837e1b51948f *man/transite.Rd
5adb17e00b760f73e6992e4e8c38bb15 *src/RcppExports.cpp
ee946b5be3e5f2a0a19ec949ee957972 *src/scoring.cpp
65ec1e9e8302abd64132571e8492fa91 *tests/testthat.R
eb8df474e660c2e85aa52148b2ee8df7 *tests/testthat/test-combine-p-values.R
4b710a39576405b97431d9629fee802f *tests/testthat/test-k-mer-based.R
65f98c89cf539bc6fdfb4a5513df48b6 *tests/testthat/test-main.R
d3858822667eff6cc867f2c667ae0434 *tests/testthat/test-matrix-based.R
3e81132b271a1e178df871e59d69fc26 *tests/testthat/test-misc.R
beb0c4796d066d2a9ac9ee073f853f0c *tests/testthat/test-spectrum.R
839f2406ec6bbcc4f3109ce3d8b8ba65 *vignettes/spma.Rmd
