4ec8934cf95129a72d91703bb8e5a287 *DESCRIPTION
c4c131d02f28fccba179b61a718527c5 *LICENSE
cc21cd4d5ba44c60dcffebda04751d34 *NAMESPACE
12586cb603c1c5761cd8383a460e425c *NEWS.md
bd8be3df762ae36ecc49e17ebca2f80f *R/data.R
0ed13b492f10351ede8a78ca8ce7f2be *R/dimension_reduction.R
b967473e2f00b79030de577026b8f5f8 *R/generics.R
b1aae2640f29e7f32e0fd3d217f94c9d *R/motifs.R
f49ff35519fa21ecb540c28693170984 *R/objects.R
8850a66f0481e182d9170033eff3f5aa *R/preprocessing.R
47290ec93f2aae67e5f58ccabe829d75 *R/utilities.R
534079d6d10e2e4fcf225bc496cac715 *R/visualization.R
c4d3e5a59648dac68d80a5787e19452b *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
b193d61b261df927c5a25bc84d4e0181 *man/AddMotifObject.Rd
715d944fd0ec964accc3c3d91b67c64c *man/AverageCounts.Rd
ddc763c661da12993c920370f72b99f8 *man/BinarizeCounts.Rd
92ddcf5ef51cab9b15506fbef1b69486 *man/CellsPerGroup.Rd
9d92dc498dce1845240927754c063f56 *man/ClosestFeature.Rd
05a4623bb44ce97c23d0a3ffdc103fe8 *man/CountsInRegion.Rd
ae642033adc2644b881a63c38a4592d0 *man/CoveragePlot.Rd
06aefa68a94885d01645a7adcfce4df6 *man/CreateMotifMatrix.Rd
405909deb8c6e87d02bcc37a8e75c33d *man/CreateMotifObject.Rd
2b30282668090118f764071c9a6c5fc6 *man/CutMatrix.Rd
29e0161c009c5398052880879c350022 *man/DownsampleFeatures.Rd
db8e8229fc8d00aaf9f2d5ffb64e89da *man/Extend.Rd
6547aa53a5390f5ea4bf1c634dcc500d *man/ExtractCell.Rd
828662378dbdc8c8f796eb3cfc5bedf6 *man/FRiP.Rd
11b5604b30cfc9695fa38fc0954cbe9b *man/FeatureMatrix.Rd
9a86ab09b1134e7df753c63160ef3744 *man/FilterFragments.Rd
418e3fba4c471ae0b83beb294d938c48 *man/FindMotifs.Rd
08ac7d0c7ff3cced93fd82577f0911f0 *man/FindTopFeatures.Rd
03eddcc070d4c33d6efe72b2a9da68b0 *man/FractionCountsInRegion.Rd
a0cd4c4252390f62a42bea5af1450fa0 *man/FragmentHistogram.Rd
79d8efd88b66e3e291dc59061c159f85 *man/GRangesToString.Rd
cdb1a7d02fa7ee243693e9ed90b3693b *man/GenomeBinMatrix.Rd
8cea9bee06c32caa7707c7f4aeef60cc *man/GetCellsInRegion.Rd
ddb6bd95ad3b82cd8a64d10be1eb6943 *man/GetFragments.Rd
93ce66cfec6e38f88538a386704b2249 *man/GetIntersectingFeatures.Rd
0b19068e02ecc89d6858d48670895485 *man/GetMotifData.Rd
175f37142637edad704b3aa249e88a3e *man/GetMotifObject.Rd
f20c9bf81893b7ba6b74324f1b4e0eea *man/GetReadsInRegion.Rd
2b2e936ecc1dc563e9759d168f3ca4c0 *man/IntersectMatrix.Rd
85c452c0d463efad55994e27cf587ad9 *man/Jaccard.Rd
dd93eedf43a340187cdc4b8f1b66805c *man/MatchRegionStats.Rd
39cc0b0f84bdffcbb7458c955ca10b1c *man/MergeWithRegions.Rd
06543b207ef0f92746f4235ee264fa49 *man/Motif-class.Rd
36c300f544214926614e0c15b2bdd14d *man/MotifPlot.Rd
a02230da491596d650fad8476973ce67 *man/NucleosomeSignal.Rd
e3b971f82fee25faad85b2fe573b38e7 *man/RegionStats.Rd
21b595f24063619613782acdcc983a21 *man/RunChromVAR.Rd
85420340576654c114db8fdc3a2fb6d6 *man/RunSVD.Rd
dd4f9d973206a4bcbfe9a4cb9d1a7112 *man/RunTFIDF.Rd
df8c3d4726b6967f15db27e10e2882bb *man/SetFragments.Rd
9e3419744a78aeed0a463867bd39d4a7 *man/SetMotifData.Rd
ab106d72d9dc33f6ce9f4eca6934354b *man/StringToGRanges.Rd
da2b9a029faf3fd31565ad9c76c201f2 *man/SubsetMatrix.Rd
d150cc2f02c3b2ae15190e45f00cb3b0 *man/TSSEnrichment.Rd
79f230d6ac5cfd9f594fda951fbc3769 *man/TSSPlot.Rd
34e38c9fd754120182edc29316cda641 *man/UnifyPeaks.Rd
9164eb9d5cbef677a3c2c7679afdf343 *man/atac_small.Rd
7315721e8cc4efc0ccb0af82b136241d *man/blacklist_ce10.Rd
dfc527eb173c01f2089f1f84e7cf6b6d *man/blacklist_ce11.Rd
68d738cfec0e2687b6e403d3abaec9a4 *man/blacklist_dm3.Rd
ec556699075a20e83ee51dec474b9332 *man/blacklist_dm6.Rd
0f3a224cc651913d8783f66540af42f8 *man/blacklist_hg19.Rd
eeed932cc4c5d5988c58d3f0ec75cf2e *man/blacklist_hg38.Rd
725cd1b27ca79b030ea2cc9887113362 *man/blacklist_mm10.Rd
c39caccec31230f56bb5a2d45b4239cf *man/subset.Motif.Rd
2708ba958c1510e975704ec3af9e7d0a *tests/testthat.R
8a52a69a40fb3083386eb1657e884d25 *tests/testthat/test-dimreduc.R
fd78959128702ee63a9f1eb95428191c *tests/testthat/test-preprocessing.R
9c05a5d9e925b7c52fee17f5c4bd44cc *tests/testthat/test-utilities.R
