a5b1db155156a0e51c4dc2ec5457aa4b *DESCRIPTION
def8289201f5fad0ff28f3c66036b135 *LICENSE
4b6d49bbe77cf7984968dd1ef1439ce8 *NAMESPACE
55d4c2fbda4af4be12535fc165f0108d *NEWS
9c0f0e0442a152cfa7780acc5d852372 *R/AllClasses.R
639519d8e4b880a1a7b43f96a15418c0 *R/RcppExports.R
c11f58d1f7fc8bf509516bc36643e3d3 *R/background_peaks.R
35227d2354ec9c4ff3b4e0cb7a0bb441 *R/chromVAR.R
fd1fcce988dea87df0fdb2e19dd4fd38 *R/cis.R
15f167861cae54bcaa5bcbb83fef12a2 *R/clustering.R
b141f55b6a581b402d551898c7d6b89f *R/compute_deviations.R
1f2242c3e96b4d679e6e8b13cf4afc87 *R/compute_variability.R
03f67c7b1033fee3121d72e176375bdb *R/differential_tests.R
2b017a41dbea4ea1036c20a75262b39a *R/dimensionality_reduction.R
21ffae8941cbb757838cc744708a72c1 *R/filtering.R
a0112af5505af5267ebf8a34f110c873 *R/get_annotations.R
acad7b25e0142dc38f679321c7dd22e5 *R/get_inputs.R
b4327c294d32085a4a4e9d0255daf184 *R/helper_functions.R
52a4988a88da3732739874aec2add745 *R/kmers.R
7359bbd06379b9392a593a69078f50ed *R/match_kmers.R
0c0734464f9ec0409e6a23e61c8c68bd *R/motifs.R
126ad2673d90e8442d619df4c7e63269 *R/plotting.R
6957f29aa7ccf5d78fc4c27d52b657c3 *R/pwm_dist.R
5cf6eea71a4bf21caa08fb6dc6bae0d4 *R/test_sets.R
36d0b5c1ec470888defcbf0dc0b640cf *R/utils.R
0d137dae80823918e506451c64d9a38c *R/variability_synergy.R
b074064fde5be63564a25fc7bacd0424 *build/vignette.rds
a5f82d2afbb8a69076ed7df77922db7e *data/example_counts.rda
3144a553b2c9fa44b9c9bb0e4df91a01 *data/mini_counts.rda
4935e18f999bb822f299d4252533c2f1 *data/mini_dev.rda
9aa4d98bd6d521ebe1e266d6f1189849 *data/mini_ix.rda
39034a022b44b71accb8a114e57e5be9 *inst/CITATION
071d0fe81379ef8aade527dfc6c23e5a *inst/doc/Introduction.R
e647fb1ca704e41c4dde1a28c3699c58 *inst/doc/Introduction.Rmd
4a72a2f212ed6d89afa4fe117e2de837 *inst/doc/Introduction.html
37671395b9c407b9ed11352bc82663a3 *inst/extdata/counts_table.tsv
7ce6288e99ae8090330521cb7abc36c3 *inst/extdata/deviations_test
53b91a90f865db1aa8962e74070bb50d *inst/extdata/test_RG.bam
dd22824ae0fda9c8a28a56b6086e299c *inst/extdata/test_anno1.bed
a6f21fe0ee54c6b2ef11554813855bfe *inst/extdata/test_anno2.bed
dffb9788cdf37768e4c7c79a5778ae1a *inst/extdata/test_anno3.bed
ac7477a2442c78df7f6fe512c1cf2f24 *inst/extdata/test_bed.txt
0758f21767f496e0ac79ce0a5f1c081e *inst/extdata/test_reads.bed
ce6a7cb84bea1705a346e7cee91f227f *inst/extdata/test_single1.bam
ac67fa8497bab48baa76dfb26377c085 *inst/extdata/test_single2.bam
6a3b3010792c48ae4ea1a0e23987d89b *inst/extdata/test_single3.bam
b6e3fe53ae6fb6d4e36b5a84d93445b8 *man/addGCBias.Rd
eedc4d3004e28a4a53b02401904b611c *man/annotationMatches.Rd
ec707391c54b526e4bf1b4de48b8fe17 *man/assembleKmers.Rd
e1ac40ab873d1f06aca21e946c1ea709 *man/cbind-chromVARDeviations-method.Rd
01509874f288f156c817d658862dd0b0 *man/chromVAR.Rd
2db8c4119a50d00dd6bf60b7ad8ca20d *man/chromVARDeviations-class.Rd
8fdde08abc3761a5bc4ffcafac41dc8e *man/chromVAR_theme.Rd
4921888d90a432714dbe987568d02416 *man/computeDeviations.Rd
22b869a047f3c29fcbe5ec27c2eef1cc *man/computeExpectations.Rd
fc5495121a490b6ae51a8afd07c78077 *man/computeVariability.Rd
090eaad180232ffc7b76c8e3933d82b5 *man/counts.Rd
6dcac9e711bd544571496ce5e977444c *man/deviationScores.Rd
41b45bbea2393be7b2e831ee0c1eb30d *man/deviations.Rd
fd8bc11e347722461931c210a1957a80 *man/deviationsCovariability.Rd
168f33ecefda2f69e11ed46df6fc888d *man/deviationsTsne.Rd
f8e1a3fd8184aa72fddb081950f5fadb *man/differentialDeviations.Rd
d3efb5122f40f13f70d9e152689987d3 *man/differentialVariability.Rd
df052d703bcc45844850ed5349371b3d *man/example_counts.Rd
5e23514c14882c6a46f6640ecbb046de *man/filterPeaks.Rd
56baa41b74b4ecd7ac28ac0f04f4b20c *man/filterSamples.Rd
2506968e043bfcaef8a7ddb7d6373b58 *man/filterSamplesPlot.Rd
660cab1ee3c8095a5da31f1cee6626ad *man/getAnnotationCorrelation.Rd
0f735411615250d023b61384426691ab *man/getAnnotationSynergy.Rd
bd0d823e8dc90fd337bee8d080b07068 *man/getAnnotations.Rd
4b50b9f7b07dca729eacdec6df263575 *man/getBackgroundPeaks.Rd
4f5c03ec0405691b2d125553ad7827ec *man/getCisGroups.Rd
41a11d5f119e3c45704d13e57b48724f *man/getCounts.Rd
cb620d5840893d62d2fe8a9e9952d648 *man/getFragmentsPerPeak.Rd
ee780f783b8f440841353a910596a1a2 *man/getFragmentsPerSample.Rd
1575a072cd3e2ff91da3be6fce5353d9 *man/getJasparMotifs.Rd
a10a5a01f85ce471544b3a39048d9ba3 *man/getPeaks.Rd
b4f5cc394e0c5e1bf2340c15b34522e1 *man/getPermutedData.Rd
afb265d4adc991c2ff5b436f0949df25 *man/getSampleCorrelation.Rd
392259d4b3e466f0d66a69f527d17dec *man/getSampleDepths.Rd
65803c030ed86b921bc40589c92318ca *man/getSampleDistance.Rd
c335d40941d64eaad168c87c6a41dfb9 *man/getTotalFragments.Rd
cfd7b72b4551e2c7bdb776f2951f657d *man/makeBiasBins.Rd
7e4e52f5934756e8664110bed6c8c382 *man/makePermutedSets.Rd
64fa6c208e4dd2a29307f06e3d73ad69 *man/matchKmers.Rd
2bf4eb5314b604e261177cba93dfefdd *man/mini_counts.Rd
8f63d80c1813a204f06f850f5c24f887 *man/mini_dev.Rd
e54261dc6fe8c62434080792666723aa *man/mini_ix.Rd
14b40497ed1a91d5afd3a754a2a2ad6a *man/plotDeviationsTsne.Rd
5755dbfb08a6140c1bb3f4e3d5b9dbaa *man/plotKmerMismatch.Rd
e188056e1ecc14149f2b82627ef6c441 *man/plotVariability.Rd
79343728296c870c49bbcb8f05541709 *man/pwmDistance.Rd
8a476e50b292eef7694d3d3a3c1f2f6d *man/rbind-chromVARDeviations-method.Rd
85cdaae268a40e641cac9a9fc541319c *man/readNarrowpeaks.Rd
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
1ab0a0c471e87d3a057cf125572f8cf9 *src/RcppExports.cpp
6282f051f5a78a9607175166cf29737b *src/pwm_similarity.cpp
76c094286d7a38de784857aee2a51540 *src/utils.cpp
29c570149bd773a250de55477430dc00 *tests/testthat.R
33a0048ae640fbf7a3626bc6ff71eb15 *tests/testthat/test_compute_deviations.R
0b6d6ceee49242b3dd7e34cb125e796d *tests/testthat/test_get_annotations.R
4ba39eea2051d06add1d27bd13fd7e97 *tests/testthat/test_get_counts.R
07f271853756bd1e1d7946c43abc2819 *tests/testthat/test_peaks.R
e647fb1ca704e41c4dde1a28c3699c58 *vignettes/Introduction.Rmd
