beb76680d6c41d429d85941142d99f08 *DESCRIPTION
157b27cb9e067fb326dbd9821dfffbdd *NAMESPACE
b22dae873051ddeb3605950a1c821d6d *NEWS
1b24dc780d6c7f81258ad65c254bf5e1 *R/AllClasses.R
d7d64c1a114678ede14c70137881628f *R/AllGenerics.R
52888e48e8809ed1d0e064b28b861e93 *R/AllMethods.R
7412676a70afa5dc547bcde43346985d *R/UMI4Cats.R
b01556b23036f3f87a452472a2f4c4e9 *R/analyzeUMI4C.R
212b9a6d410ea9b88e79b18c56c53b17 *R/callInteractions.R
b9c814d9d6c7a398cae53056b501ac16 *R/contactsUMI4C.R
379ee75a1350cf02e2be73a112ebee3b *R/createGeneAnnotation.R
0c65daeaca30c2ad12dc19175db038c8 *R/demultiplexFastq.R
64988fbe166ce38bb2196bcbb53aa8d4 *R/differentialFisherUMI4C.R
fef48e6e2ac7bf935e9ee264337d8e8a *R/differentialNbinomWaldTestUMI4C.R
e72c8a9029c40d075f2ed1d6f9573f97 *R/digestGenome.R
c1f7a0da090f6f7661675ecdb6e6330d *R/downloadUMI4CexampleData.R
7d8c6f334ad01490eeab5dec29dfad6b *R/getViewpointCoordinates.R
ca5500d4b774d170f0879e086dd8b8db *R/groupUMI4C.R
555f548da06bc0d171c618ecce805bf5 *R/plotUMI4C.R
9e18f55d9e0fe69bf71398d04bd77392 *R/statsUMI4C.R
6d937abd3885ec6df401334f84ed3f68 *R/utils.R
7d6a1da51c8e4a8f8000c101a5a9efc9 *R/waldUMI4C.R
eacf50c0def28c55b8655a764569aa46 *README.md
5ba9c2b6e2244ada2d91ff7951bdff22 *build/vignette.rds
54335866f7934782cba3d55989a9491c *data/datalist
18ab29db9658ac14fcc504bab0ca3676 *data/ex_ciita_umi4c.rda
9d6b1e1d2413bcaa0c2d7935cf7b7f1d *inst/CITATION
4c09c10c40e3c86c8e31c733856f49bb *inst/doc/UMI4Cats.R
48bb1a909e798e13a071a4cf93842ac4 *inst/doc/UMI4Cats.Rmd
f22462da5f8a0a8a1bf9773947e7bc5a *inst/doc/UMI4Cats.html
433fe163ea0e3ab3084b7df8c6c61c2b *inst/extdata/CIITA/count/ctrl_hi24_CIITA_counts.tsv.gz
fd2198b1bd1bc4c9416d5dc1120c8475 *inst/extdata/CIITA/count/ctrl_hi32_CIITA_counts.tsv.gz
3d69b17111e6be943b3b24774e7cee57 *inst/extdata/CIITA/count/cyt_hi24_CIITA_counts.tsv.gz
dcccf576b93420fc243825189256e5be *inst/extdata/CIITA/count/cyt_hi32_CIITA_counts.tsv.gz
823f3661079b8dd42709c31ce0339039 *inst/extdata/CIITA/logs/stats_summary.txt
40d7c06bd11eb7ec9d66d9ed9e266918 *inst/extdata/CIITA/logs/umi4c_alignment_stats.txt
59d9b0ca7564e1b7a2549ffa75038798 *inst/extdata/CIITA/logs/umi4c_stats.txt
da6121c5143c04ecd430d1727c3ebe23 *inst/scripts/CIITA_generate_reduced_fastq.R
dedeca59e6abee3ef228bdafd28921e3 *inst/scripts/CIITA_process_example.R
27672068e007ce897b2e6e7016c76b0b *man/UMI4C-methods.Rd
82a24e8bc7d08a37372d75f9c8c890f3 *man/UMI4C.Rd
dcb7bd4d8f998fe56e41df3144fc4745 *man/UMI4C2dds.Rd
3f0ce36e8d5bd898b8280bd5cd542ebc *man/UMI4Cats.Rd
67e33e44b9a3ec96e4aa526466c320c3 *man/addGrouping.Rd
548dd6be8bae1d399022fe0b24a68660 *man/addStepping.Rd
b667565ccd15eec3cac515d9f116d9fd *man/alignmentUMI4C.Rd
0b74e97e3f44463bc66266fee93c2d78 *man/calculateAdaptativeTrend.Rd
a01951a6ff00f5c51407a96657d66823 *man/calculateDomainogram.Rd
dd4c26b3c3fec548f44906938630bd5d *man/callInteractions.Rd
095b9adbab5ea341b67c02020dee023b *man/combineUMI4C.Rd
7348dfb6e570e642eaf4d6bc670f71a3 *man/contactsUMI4C.Rd
c8acf6a3fa38f588f987a13487440cb3 *man/counterUMI4C.Rd
c410e8f2f127dfeaa1cfa13a02774a98 *man/createGeneAnnotation.Rd
e0412bb0386b5e5506855dd117805d67 *man/createStatsTable.Rd
41d651953534f200c03d1c0c8e73116b *man/darken.Rd
c3cd24fd529adcccd861e472af3130ff *man/dds2UMI4C.Rd
941f08a040cee5bab05edba832f27560 *man/demultiplexFastq.Rd
20682c6f043412256bbffc38bcaba9c0 *man/differentialNbinomWaldTestUMI4C.Rd
dc1d66d6202164d68d98b099451e7318 *man/digestGenome.Rd
02431e10e376af0f9989f585a62904ce *man/dot-getCache.Rd
52237844f3b5d6b33df1c7fb360035f5 *man/dot-getSummaryBam.Rd
14c93d5e639c49934e71e9bf9bef91ee *man/dot-singleAlignmentUMI4C.Rd
e8ab8a76c923ac535a1affc323eca939 *man/dot-singleCounterUMI4C.Rd
c03e71d1bc39269df9201366c5a02208 *man/dot-singlePrepUMI4C.Rd
015c13477f38200ebc1c75c20f7fa6d8 *man/dot-singleSplitUMI4C.Rd
2ea37ea9f3e7f997c6a9ad35eb5db0c5 *man/dot-smoothMonotone.Rd
569507e6d469d9da645d96758c3f016e *man/downloadUMI4CexampleData.Rd
209958fbff4e7346e990ce164766a01f *man/ex_ciita_umi4c.Rd
fe5f7906dc643c0983585233455ff7e6 *man/figures/README-analysis-plot-1.png
153d676cc8df1da20e6c8f94cf5cbec9 *man/figures/README-analysis-plot-2.png
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5c55ab32adf41d79dd20583b4abd69ae *man/figures/README-unnamed-chunk-5-2.png
7c66db7c904f6a854ee90d845ed1ad39 *man/figures/UMI4Cats.png
5f0ba4ee3a51cc7ca52f46adcea9092f *man/figures/UMI4Cats.svg
58ad009cc3d914717f15728321748f56 *man/figures/logo.png
0d36bc6dac6d6f55197c2a0e8ec4ce0e *man/fisherUMI4C.Rd
16ec04ffd141cc9cc80d6d9d34430f6a *man/formatPlotsUMI4C.Rd
5a0e8cb3a2747d82a89626f4fcc579c6 *man/geoMeanCoordinates.Rd
41474cb6f065789b7be7799a5d004cdd *man/getColors.Rd
71abab1da1f6d7c692484156b52b1ff8 *man/getFactors.Rd
13ab35d1c94a2a78ce89a01ff9fdb40b *man/getNormalizationMatrix.Rd
ea47bba0a68f001c8a3505bec1a2ef79 *man/getSignInteractions.Rd
4e8de280fff9ae4b92a3ccadaf2d51e6 *man/getViewpointCoordinates.Rd
4a7f80a7487c2b0315d2c23d3bbb6711 *man/groupSamplesUMI4C.Rd
be3d1ddb30cdb19cf2549c4511cb18a4 *man/makeWindowFragments.Rd
9699c7d13f65b6a5d260ec1b6ed9b1da *man/nbinomWaldTestUMI4C.Rd
8c1413a5f31c1b4b2f5f96d6fdc8f813 *man/plotDifferential.Rd
29b2b3743f33d7d5e22c9dae84682e17 *man/plotDomainogram.Rd
87f1abd8294d66c4f5d16b11d4c1b35d *man/plotGenes.Rd
f56a5d67e7100c88a3fccdfc2779ecb4 *man/plotInteractions.Rd
c5ac494bf50e11f93e10a700341d25b0 *man/plotInteractionsUMI4C.Rd
e9afbe2bfa2aef6e098b40a7c0453d89 *man/plotTrend.Rd
d1c3c82150c258f216be383f03b2ae25 *man/plotUMI4C.Rd
2c4539aca18dc2e93e296432db31ffe6 *man/prepUMI4C.Rd
d0ed2c263d85f3d960ff33ef2180dcd8 *man/smoothMonotoneUMI4C.Rd
962032f378d8100c6facd91242037216 *man/splitUMI4C.Rd
236bd873390c77fd358fb1f096490177 *man/statsUMI4C.Rd
e384a1a592add15f62b763d3ec4886c5 *man/theme.Rd
34d7b0ff88fa15fc50b19665bbe19b0c *man/themeXYblank.Rd
631429f1c0af5cbee6cf3898dfb0279d *man/themeXblank.Rd
7d4cafc02d36c58976bc7a9d36f5b780 *man/themeYblank.Rd
491347b5c560a2a62764dd9a74870e2c *man/vstUMI4C.Rd
d97e43fb65af8ed3d1f39f5c6c09831f *man/waldUMI4C.Rd
d31e68a32a56958da3bcf9a7f8078e50 *man/zscoreUMI4C.Rd
9a6d346f4a7681db9c03569a34c011d3 *tests/testthat.R
74c68dc6dedacb93c4408abf81e44f61 *tests/testthat/test-UMI4Cclass.R
e84164eae52abbae2f521cb13498fbec *tests/testthat/test-contactsUMI4C.R
e8b19bd0226ccbd1c1c0a08d19de5963 *tests/testthat/test-createGeneAnnotation.R
f482d1c7a34746e39d9edda03a8a1e06 *tests/testthat/test-digestGenome.R
52712a00354f834ae27b8dde2fd262d6 *tests/testthat/test-downloadUMI4Cexample.R
2e6433e27800e4ee5c587bde09d18cf5 *tests/testthat/test-getViewpointCoordinates.R
656a992891b0ca934f0a73e85463b0e4 *tests/testthat/test-statsUMI4C.R
48bb1a909e798e13a071a4cf93842ac4 *vignettes/UMI4Cats.Rmd
7ab88a8db277729771a688e3a3eeda08 *vignettes/bibliography.bib
6e7bbb8b0d95094faa6f3e182c6346a1 *vignettes/figures/differentialNbinomWaldTestUMI4C.png
585719288e78bc92a2c2afe332025735 *vignettes/figures/differentialNbinomWaldTestUMI4C.svg
58ad009cc3d914717f15728321748f56 *vignettes/figures/logo.png
21f3304b4acf1b52c4e88b5ecf7d0ad2 *vignettes/figures/read_scheme.png
ff6d1877830b776f435590d4ee3f4b1a *vignettes/figures/read_scheme.svg
5d7e4cd365271d784ce8e8c34613b99d *vignettes/figures/scheme.png
5f3f15de1a3b9d9aae952e31d11b76ce *vignettes/figures/scheme.svg
