f70e9950196827675fb491961e44a26b *DESCRIPTION
c4c131d02f28fccba179b61a718527c5 *LICENSE
cfe53c445b6edae515927d6123de1a23 *NAMESPACE
cbc9e2f82a87f9c5f69eb699bfdeffaa *NEWS.md
bd8be3df762ae36ecc49e17ebca2f80f *R/data.R
603a392c7b6fe064b8bffb88779a1aa5 *R/dimension_reduction.R
48894f5267edf909c518d647c46012ad *R/generics.R
b7bc92df7a5ce4a480cf11d66d4de6ef *R/motifs.R
3aed8ba4bf9a6424e8cbd1673dc509ea *R/objects.R
248d7b4849a8da787520a68189ffb714 *R/preprocessing.R
fc0b37e6450d88a8f7c7ae808caac5a8 *R/utilities.R
90495dbb6673980f517a9997b7479ef7 *R/visualization.R
9923c0768b0475416062499ccd12f4de *README.md
793b72cbc2dcf6e5c4a622ce6fa25b92 *data/atac_small.rda
e44ce034696b2a7650c4c103e848a7cd *data/blacklist_ce10.rda
84116d6460f16fad743f6eccfc923c63 *data/blacklist_ce11.rda
9cedcbeaa9f92aafdc59986d77475023 *data/blacklist_dm3.rda
b5a7cd786ba389ab851502a6a74fafe3 *data/blacklist_dm6.rda
67d0ece372cec5b3bf8d0afec6f50ae1 *data/blacklist_hg19.rda
a8393a223bb605d71ceb835e11b15f7c *data/blacklist_hg38.rda
7e432170b3d2fbc25d558ddf6d1ecf7e *data/blacklist_mm10.rda
26a0f5eb639885c6c1f1a9a4839041e5 *inst/extdata/fragments.tsv.gz
df1eeeaeb35987e59fafad9e2cd74ab1 *inst/extdata/fragments.tsv.gz.tbi
934e5c8f817e532106ea08d37f552127 *man/AddMotifObject.Rd
715d944fd0ec964accc3c3d91b67c64c *man/AverageCounts.Rd
ddc763c661da12993c920370f72b99f8 *man/BinarizeCounts.Rd
92ddcf5ef51cab9b15506fbef1b69486 *man/CellsPerGroup.Rd
99bae710cf74ac48c9825f2c61b08b9f *man/ClosestFeature.Rd
1592278ab6fa78b00b73acae893780b9 *man/CountsInRegion.Rd
ac5b932320ff84018cd05e4221d1f528 *man/CoveragePlot.Rd
8f4846683d51925153403e9eea8ee064 *man/CreateMotifMatrix.Rd
dd6d93e4ca73fd9a20c9479fe30d04ac *man/CreateMotifObject.Rd
69daa34f8dd80c3f7e90f968bef51447 *man/CutMatrix.Rd
54b3323a95c18b6f2d5010f74ae77a71 *man/DepthCor.Rd
b265e36c36d914f48fd1d8fb46e4b79b *man/DownsampleFeatures.Rd
db8e8229fc8d00aaf9f2d5ffb64e89da *man/Extend.Rd
6547aa53a5390f5ea4bf1c634dcc500d *man/ExtractCell.Rd
a9228813f8d5dde979b750bb93830586 *man/FRiP.Rd
aabac8eedf8732c9e17884d01c2a7841 *man/FeatureMatrix.Rd
2943ba979c205bd58d3f9b2b2d69a800 *man/FilterFragments.Rd
d2e57b79a40f6d4d1bebc4d493235cda *man/FindMotifs.Rd
49c5fb6263b899eb1ccf604dc5fe7876 *man/FindTopFeatures.Rd
9431a00b655d40142474493a43b51b79 *man/FractionCountsInRegion.Rd
b22a9f3ebcbb5c8f930cde36d1b8239b *man/FragmentHistogram.Rd
37b623fd4ce8f6f315839248a80565e0 *man/GRangesToString.Rd
ea7cec656f486977db2f449bc0b27d49 *man/GenomeBinMatrix.Rd
ae23a7ec667c5b25d02b6206a3c74ae9 *man/GetCellsInRegion.Rd
b42fe32e17b7aeddd106905e4f5ea908 *man/GetFragments.Rd
2efd3ed80f08d5cb15d0653ca9abf88a *man/GetIntersectingFeatures.Rd
0b19068e02ecc89d6858d48670895485 *man/GetMotifData.Rd
175f37142637edad704b3aa249e88a3e *man/GetMotifObject.Rd
5beb64f606d15e26b9fa2621a9e9e5f9 *man/GetReadsInRegion.Rd
f11126f144fe7328586961ff234565a5 *man/IntersectMatrix.Rd
1d278d6b2b9ef64b8e5956091709416a *man/Jaccard.Rd
254cf3fb6418aab2f8bee055b30047a8 *man/MatchRegionStats.Rd
61ba0c392421269dd070c56d584fbe45 *man/MergeWithRegions.Rd
06543b207ef0f92746f4235ee264fa49 *man/Motif-class.Rd
36c300f544214926614e0c15b2bdd14d *man/MotifPlot.Rd
07d1221b60d7839183b031acd2d0f83a *man/NucleosomeSignal.Rd
a991e0e0d9c1b981691e8c3caa0ca89e *man/RegionStats.Rd
b48e432e4c3f92fac6f1159baf39c323 *man/RunChromVAR.Rd
48ab00e110a50c6d347c807fcfb71de3 *man/RunSVD.Rd
82f4adde99dade916751751d0fb408f2 *man/RunTFIDF.Rd
7d7a6cd052895ac69e78eb8cacbc8de4 *man/SetFragments.Rd
2421d2b0f280c5a0311f8ce82dcc9b8d *man/SetMotifData.Rd
96e86066f450ea6265a9eb8d4fc26e2e *man/StringToGRanges.Rd
b629586e40c6935f6cfb7ca5094fae8c *man/SubsetMatrix.Rd
a9102884ce4cb5e89b2c9fd04312418b *man/TSSEnrichment.Rd
7b64dfd7ddaa2ddfe858b31014a0b2b4 *man/TSSPlot.Rd
6309d3af00a13b127f2602eba12c78d9 *man/UnifyPeaks.Rd
1d4cc06082cb7154f46a6d9056528b3a *man/atac_small.Rd
8f0e2ef4158f3dcca7c1ae28596750c1 *man/blacklist_ce10.Rd
e1a1503587b2e3d7471e57c4acb70dd3 *man/blacklist_ce11.Rd
87d15e8f74883addfb9af06046b24669 *man/blacklist_dm3.Rd
0a478dde3cf707a927022cd876ad5c26 *man/blacklist_dm6.Rd
aec27c1e46d96e09b81f698a063af66b *man/blacklist_hg19.Rd
68e4a8dff80f6894ed00fe0455513fcd *man/blacklist_hg38.Rd
5e8c5e2dae713f5fdda4c35bea7e1074 *man/blacklist_mm10.Rd
c39caccec31230f56bb5a2d45b4239cf *man/subset.Motif.Rd
2708ba958c1510e975704ec3af9e7d0a *tests/testthat.R
1a8606af67fb3a22bf870dfabf224062 *tests/testthat/test-dimreduc.R
d6e25eb4e85e30ab2e756d380f536432 *tests/testthat/test-preprocessing.R
08648fb7044321135d977e0b84d20a3a *tests/testthat/test-utilities.R
