7bfae7d5e2e3af554e3c4701271bd573 *DESCRIPTION
c08f695f341400baba0136c8542b9f7d *NAMESPACE
f3213b19cb983cdd08f8d802b2ead16b *NEWS.md
fc63a53c409fff5fd023b5eb1787d34f *R/addAccessibilityShift.R
c962816365452010f5a3fc7850f8946c *R/addMotifSet.R
faed1d529c3810648d5aa06529bf4fa7 *R/annotateTiles.R
d670fe5cd8d3f94b575e4de825a9ea1e *R/calculate_intensities.R
61db254e27095cbb86924cd0c8109161 *R/callOpenTiles.R
ea1a412c34de90699eedaba4f511a785 *R/callTilesBySample.R
5e12b1c7369d4e350d990ff233429d8a *R/co_accessibility.R
59ec918218d133e4c007218f32212090 *R/coverageFiles.R
375d5403bd0457c54dbbd2a55437ddd8 *R/determine_dynamic_range.R
3c325e6279a9a93c632a045edb3c83ed *R/dynamic_bins.R
9d9c9bfe53f60f0758485dedec3fd404 *R/estimate_differential_accessibility.R
3f62c1e1019ed7abc93b79bdf8f494a0 *R/extractRegion.R
c5eb7bfeff35be34380972f0c55fbc42 *R/filterCoAccessibleLinks.R
4e228a4f86c9b53f16469978432990ff *R/getCellPopMatrix.R
a0c998f1496f1ebcadd878cbb7ee3199 *R/getCoAccessibleLinks.R
1585337ad850633bb3bb77fc22c5954f *R/getDifferentialAccessibleTiles.R
052de1a7568adeb1559c71fd66e03190 *R/getPopFrags.R
8805b2e734d4e496516b2835729db75f *R/getSampleTileMatrix.R
9ac1846ba5d19472136fa3f077072fa9 *R/make_prediction.R
11f02a646515d09f313bfcf9a11892c5 *R/models.R
d2507c84026b19c7f74c9de02d0f2bcf *R/plotConsensus.R
7b1c3b753c26181c998f4ad507f8cff7 *R/plotRegion.R
2d0ff66ed4e6c558f6030f92f9a841d3 *R/plottingUtils.R
15cd180ca9cd30d11b96535e20f0d804 *R/singlePopulationConsensusTiles.R
ee57325bfc29a578bb3e9a0aa9aa7312 *R/singlePopulationSampleTileMatrix.R
c3ef7117f0c5fb7b1976e83499da9eee *R/subsetMOCHAObject.R
a4e9c98988aae0288c4e628182c53d5c *R/sysdata.rda
520de2530279d1c24cbab4b7625a7be8 *R/two_part.R
8611b678192dffdb181d760a33fe6c6f *R/utils.R
604a413f774cfa1f4b22a0f635812402 *R/zi_spearman.R
129e478cf53c66c37b740e497796cb2a *README.md
6d185a6639ae646f9e4884058d2b5be1 *build/vignette.rds
7c66f9f10d6807d8b3221f0fbb18ade9 *data/exampleBlackList.rda
58997625a835d4daf03d42ec7bd43f7d *data/exampleCellColData.rda
8e43c095825b9a443680f27a91ba1b27 *data/exampleFragments.rda
24367691d4d5995b0b7db0f65dbb16b6 *data/finalModel.RData
b1b54dca99dcd8755b5f778371c2f7a5 *data/youden_threshold2.RData
efc6e65dbfb7e63aa5bf4f1fc9e1da36 *inst/doc/COVID-walkthrough.R
762fcfa75905bf11bca11a4a6d666e04 *inst/doc/COVID-walkthrough.Rmd
70420216290829f338928071a7592a71 *inst/doc/COVID-walkthrough.html
e7d05088f030914c452e576395e25db6 *inst/doc/Comparing-Cell-Populations.R
e343cc3ab3c906748721fb139fe61fc7 *inst/doc/Comparing-Cell-Populations.Rmd
f4ea6744346d6c3f28db7d559cbe26f4 *inst/doc/Comparing-Cell-Populations.html
efac6de6836be2a2b8e8e58fed729c0e *inst/extData/NB_max_distribution.RDS
450a00dd20cdbdf74f6cc5d2a4024340 *inst/extData/sample_fragments_granges.RDS
8333d6b65e63edf4d33a32ce7bcbebfa *inst/extData/workflow.png
5063c74cf9badeb3a91583b71a9a45e3 *inst/extData/workflow.svg
fa3b90a3196afd116a4f40d5f742dd25 *man/GRangesToString.Rd
021e01c8f3fdd0b662b065afa7235bb4 *man/StringsToGRanges.Rd
43dd3569b898a205abdeacc9bb121fb9 *man/addAccessibilityShift.Rd
9fbeefb2f593e3c71ac129e3db9df4ce *man/addMotifSet.Rd
639c805249feb8c650cbfda3fa95136a *man/annotateTiles.Rd
ca6929f6c376f37258b201c37f56387d *man/callOpenTiles-methods.Rd
15aa75307cf4ec3ed349946b47ca3430 *man/differentialsToGRanges.Rd
942b41f01be5083b132a290ee7b7cd34 *man/dot-counts_plot_default_theme.Rd
410174372f429c625fdda296f8873101 *man/dot-gene_plot_theme.Rd
8a5e66195c0c2648a6b899d260293285 *man/exampleBlackList.Rd
46cc11206cbe67751f8fefd7fa0c1837 *man/exampleCellColData.Rd
4a0fb97761c7fd43cf0977900f78e395 *man/exampleFragments.Rd
8fbd4ce0de2943e865a1d4942cd86de6 *man/extractRegion.Rd
f786341ca80ff2698d6f252168368c09 *man/filterCoAccessibleLinks.Rd
8387022e5f0580b22f0bfdddc567f0c0 *man/finalModelObject.Rd
45ee95d341f4af6718fabf29f998ca62 *man/getCellPopMatrix.Rd
1467901f7384bb00527ab779589d2b2a *man/getCoAccessibleLinks.Rd
dabb08ccc886539d5defc5dfe9fa05dd *man/getDifferentialAccessibleTiles.Rd
1f81fb6e098ddf1848df7c52a1fea3b3 *man/getPopFrags.Rd
5934adc97fadd2c9c34fcdab76a76bd7 *man/getSampleTileMatrix.Rd
d0d2c7935415fa903edade3f6b27cb77 *man/plotConsensus.Rd
0c2ea8c3564775b066b3e92aaceb9b0f *man/plotRegion.Rd
89cd6d04d7fe456c5a3fdbc3172d3792 *man/singlePopulationConsensusTiles.Rd
84c3040a201214230262ba56af95545c *man/singlePopulationSampleTileMatrix.Rd
d915011f1a5c4e1644d4c6f56d06f5ef *man/subsetMOCHAObject.Rd
3acfaa26b59dbc77cf92ab581c3c5ad0 *man/youden_threshold.Rd
65e8603976496124dd0e2223ebbccae8 *tests/testthat.R
b7d597a8edfa8b39ebc3dd4676d53487 *tests/testthat/_snaps/ArchR/callOpenTiles.md
e83ca3daaf89abc02b40dd827f27d38b *tests/testthat/_snaps/Median/getPopFrags.md
08dc9c63a0d16c44ad2ae958ecac9f98 *tests/testthat/_snaps/Median_sampleSpecific/getPopFrags.md
4bb4d6f58f4623d14b4470ee845147a5 *tests/testthat/_snaps/basic/getCoAccessibleLinks.md
5f68b6b4eed21ca6b0f2d930100e39a7 *tests/testthat/_snaps/basic/getCoAccessibleLinks.new.md
36810ce208aebebb146b44dc5793c225 *tests/testthat/_snaps/getSampleTileMatrix.md
5a950153acb549d2654330d48441512d *tests/testthat/_snaps/list/callOpenTiles.md
d4e15a94e74d93a480d14a1557aad27e *tests/testthat/_snaps/nCells/getPopFrags.md
4977f19681b5afdf7d4dd8c907265800 *tests/testthat/_snaps/nCells_sampleSpecific/getPopFrags.md
558bf30086c05434fcabd19de715c078 *tests/testthat/_snaps/nFrags/getPopFrags.md
d1383b09304877b3d3d10e4bf4bde974 *tests/testthat/_snaps/nFrags_sampleSpecific/getPopFrags.md
b12c88dd8ffc67e7b5b9e9aa0ef489e2 *tests/testthat/_snaps/nrows/getCoAccessibleLinks.md
a63e3576063ed19cd66700605e38375b *tests/testthat/_snaps/raw/getPopFrags.md
f54db5729a4ddc8ba9eafcafc8bb38f2 *tests/testthat/_snaps/raw_sampleSpecific/getPopFrags.md
6c669a69d500b2a85735b1cba2defd1d *tests/testthat/_snaps/tiles/getCoAccessibleLinks.md
ca2342bc547f0973f928c90b7d2e142d *tests/testthat/setup.R
5d10e684ba295c9e8fa9d921933d8623 *tests/testthat/test_callOpenTiles.R
e891572f169f910f5c553a00866974bc *tests/testthat/test_getCoAccessibleLinks.R
0ef2be328823f85d7c94b43cfd6c53d6 *tests/testthat/test_getPopFrags.R
953f007861d922af0e18b193eea57232 *tests/testthat/test_getSampleTileMatrix.R
762fcfa75905bf11bca11a4a6d666e04 *vignettes/COVID-walkthrough.Rmd
e343cc3ab3c906748721fb139fe61fc7 *vignettes/Comparing-Cell-Populations.Rmd
