cb6aef0331d234c84e58087bc966a4b0 *DESCRIPTION
e29ecfe04d460b722168ab16c9587b45 *NAMESPACE
3574007ba8ab81a3e80a5284d8cb42fd *R/asDGEList.R
24a1c2ec8185f2860819cef2672caa26 *R/calculateCPM.R
6eed34ddfb4ccce5336c4b75cef29f52 *R/checkBimodality.R
530c2f74e6b883eae33fded7209a9b85 *R/cluster-direction.R
1732780a7eef3c28161aa7a66cec7a37 *R/clusterFDR.R
602468d15b19505d7d2c06753f831c6c *R/clusterWindows.R
8aaad7be64822cab39a75a906ed65864 *R/clusterWindowsList.R
7a031bcf3ad40d9f9971e5324df3d21a *R/combineTests.R
56db68b039603c86dd07cc4a6a51cbb2 *R/correlateReads.R
b853a77eb0d243797ea36d99d5518ceb *R/csawUsersGuide.R
803cb06150e750a9f3c5f5858780d316 *R/defunct.R
5178e73751b5bf87b3d96402d22cd36f *R/detailRanges.R
1d2ea5c30db71eaf50d8b7903f6f65a9 *R/empiricalFDR.R
1c4ad49507e2a04903768acbc52c91a0 *R/extractReads.R
dc9ac1ea9da29943329d2dadd58f51bd *R/filterWindows.R
011f312d54670cf0859effb49005c67e *R/findMaxima.R
04697d2427b9e9351209732c73bd4c6c *R/findOverlapsList.R
32cebc404d70c22acd10bda0a52790e3 *R/getBestTest.R
2a0f1eaa8104988143973af1491376f2 *R/getPESizes.R
5961da98b906d8806e39604347b9abba *R/getWidths.R
3e6bc07e20564cfca8eeec9eab6bdc31 *R/internal_extract.R
7b3cdeca9a051bd3e6c2f5b51164a1c5 *R/internal_inputs.R
e354fe36d9bfa78e6f80ddf9d8c1fe29 *R/internal_outputs.R
e5e0ffa5eaa417455037d0626a801077 *R/internal_resize.R
7a73cac7f48d1711ee675a395539c9db *R/maximizeCcf.R
cac3983fd5225d53a5c586fc07724708 *R/mergeResults.R
195ed39713dd547a2d096f10eacd0622 *R/mergeResultsList.R
4e7be21fb26fe8df671562e15356706d *R/mergeWindows.R
2cf11888312171dcb6708aa2a1ec5e3b *R/mergeWindowsList.R
47668b67934002bdf9574395ccc2b68e *R/minimalTests.R
804b8f39167d5be8dcf0149344b9dbec *R/mixedTests.R
14bc7ea78466c824a93175b46ce64945 *R/namespace.R
b684f91baafa01f23fa4378692865081 *R/normFactors.R
170fa836894ed53b1c3a11313bf5f65b *R/normOffsets.R
6940e32ded1ecba92712c81e66b82040 *R/overlapResults.R
d151fbcc1a06f50164aabc89eb66779a *R/overlapResultsList.R
6dc78962ce2d84c2e63cb3a54528004a *R/overlapStats.R
229e5dafb0d61d90d3f7835071c6cc1d *R/profileSites.R
eced379f31026d81882374d1266f51e0 *R/readParam.R
fbe84de902d92f6c48247e57f2b407a8 *R/regionCounts.R
8ed604ef26e9f3d89fe195b2c4cf7782 *R/scaledAverage.R
2dbe39e651f92cecfdf694db7ba350f7 *R/strandedCounts.R
fd6053ccd2020f316359cdff676a18cd *R/upweightSummit.R
92a89773e7851539c8fb13d6ea22782c *R/windowCounts.R
84de9748acfc9f870a3618c0452cfd62 *README.md
d690c90f870de82cc313149e0a4673c8 *build/vignette.rds
dc805ef04b2aa9bffab25468ed6f01de *inst/CITATION
f45a586f550803bafe26ff041d308e8a *inst/NEWS.Rd
eaeb6784a237f5161863af42d1583117 *inst/doc/csaw.R
b37dbf8b2a3902a6460e49c50edefef5 *inst/doc/csaw.Rmd
ec95757e554eb5c985a378cd07aba886 *inst/doc/csaw.html
3e6275988e5f3e9222b114c73fe33969 *inst/exdata/autogen.R
206eaae0892cb5679e593bc726d7553a *inst/exdata/exrange.rds
8f5785e1814aeb395ecbefbcd28b943e *inst/exdata/pet.bam
ad94f22e3930a47ed35df14ead9905d5 *inst/exdata/pet.bam.bai
aee969fd302a50783dc3f4d07265d302 *inst/exdata/pet.sam
1eeaac3e8a768c1e2e20d88f4db06652 *inst/exdata/rep1.bam
9e5e8083f8055a37c42dad4259c6f41e *inst/exdata/rep1.bam.bai
93884697c7e684680f39b6f181602b5d *inst/exdata/rep2.bam
4c9ece18e196cc1f35f17266bc11b469 *inst/exdata/rep2.bam.bai
0e07ec739c6ac4c16f9070bd26830a10 *man/SEmethods.Rd
2fcd4155ab13c4815e16a913e1c48dc9 *man/calculateCPM.Rd
21f107f2532be8916c40778df42814a0 *man/checkBimodality.Rd
bf238c224d45ccff169b66ce93e4f19f *man/cluster-direction.Rd
3572d9ae2a813075fb7e31176e6889f7 *man/clusterFDR.Rd
2fd6daee6885da388261755325c4a9bf *man/clusterWindows.Rd
7fa2c5ee53e86b8e405bd4b2c5d5c668 *man/clusterWindowsList.Rd
e5707f932bf8ad88d418c37410f9c8ed *man/combineTests.Rd
bd2ebb27eb4b3787d5f532967983230f *man/correlateReads.Rd
090f07211fdc88395c95456d76829fae *man/csawUsersGuide.Rd
ac6b741b976cb7d2383ef8c0b4f1c953 *man/defunct.Rd
a3199d738551018bc8714f25f9b64c93 *man/detailRanges.Rd
7f7735c4441ab130b7dfe06b296ccc79 *man/empiricalFDR.Rd
241e4b12c4e8ad81525225c35607da91 *man/extractReads.Rd
7909b88ffe6fc940af081f7a211221e8 *man/filterWindows.Rd
a95de2d18a92a4ada1825b2f0e086c3f *man/findMaxima.Rd
295d51401cb8d44e5810c495d0a5640c *man/getBestTest.Rd
d67821d64435dae69a6276305227c3de *man/getPESizes.Rd
650a2777854909fe8eedf8553f54e1e8 *man/getWidths.Rd
2f762eb8061ef6d0067861b6dcc351ea *man/maximizeCcf.Rd
fac1af01b4856f05b109229e9d8cedf6 *man/mergeResults.Rd
f1ec28bdb93d285e8523948a47c0ba48 *man/mergeResultsList.Rd
4e7ef097792e1d58163cd0a4e59875bc *man/mergeWindows.Rd
985ebe9213263c3757d473df5c07d61b *man/mergeWindowsList.Rd
dff489a3fec92c9580677fd981ade3db *man/minimalTests.Rd
0f3347a7a4370206fe733bb69750fbc6 *man/mixedTests.Rd
6647245d934dadb129283acfcae3599b *man/normFactors.Rd
b53d9182f6d5155285f5290a6061ab02 *man/normOffsets.Rd
fd686f1896285b723e61e06b3ada0dc6 *man/overlapStats.Rd
4f49fd01aa772c63b5273ac49e4ece78 *man/profileSites.Rd
e37f2d212b79254488dbe77e66315ba6 *man/readParam.Rd
b9dfc9e00d7b9a4c5b4cfcee5d86c2b0 *man/regionCounts.Rd
1b7797e56c82f15f1b0e0daef8d8bf46 *man/scaledAverage.Rd
5a39511f360d323a13b403098889e935 *man/strandedCounts.Rd
7c796618cedb82938cb8c22a2ef72c71 *man/upweightSummit.Rd
e6ef81a4293cc9daf0f7b9987056acce *man/windowCounts.Rd
3228ecf6925a12c2b2504aa36d485057 *man/wwhm.Rd
7b8d1c2c8939e293615971dd97729f83 *src/Makevars
45148ee838a18f189e4c553cc786cb14 *src/annotator.cpp
b74342089c3f60b698b91f2edddba5df *src/bam_utils.cpp
70e04d8b155660fc7b8c79c7d466ba7b *src/bam_utils.h
1bb16ea5541e71c3f210a72aa18166eb *src/best_in_cluster.cpp
9fcc9ce70f87c071d74d9b52bf7839cc *src/check_bimodality.cpp
35a1ae7d2afafac7f36def44e2b2e1f1 *src/correlate_reads.cpp
f8071ef1697f5357dd8023aefaf1d0ab *src/csaw.h
57fac06e3a158064b3800659a5b63961 *src/find_maxima.cpp
fb2cbb8a76a3eed1951e74c42a575591 *src/get_profile.cpp
aaf1313151a0b4197bcab8e3e0b9a973 *src/get_rle_counts.cpp
652cfd34d38209cda8ddcbab652c2f02 *src/init.cpp
a7470573872beedc07e5182ed6b171f7 *src/intersector.cpp
0317b9d4de17e0f0b0a3a00ad8279916 *src/intersector.h
cc1cf27c064b7f6273a1549f65e1d718 *src/merge_windows.cpp
2f11532358ef7a9916b580cab61b84da *src/pair_reads.cpp
b4c90cc61f64ae7c1017541811f73958 *src/single_reads.cpp
d426b09d5f728b9222224f23756c6164 *src/utils.cpp
01b641fc4fa6e4377f8187b6d3eaae5a *src/utils.h
8fa6e1d31c1a24951bfd7e911f40e142 *tests/testthat.R
03f5afe2a806f1fc535542a9cd98b0e6 *tests/testthat/setup.R
da5802c638de2fcdea59911c46c5f57d *tests/testthat/test-best.R
c5b21b3a824f23c4aa765b29435b5ed3 *tests/testthat/test-bimodal.R
59d6c81ef5bbac83c26c0548c91195e6 *tests/testthat/test-ccf.R
dd6f857c423de0e07f19b84ccbb38819 *tests/testthat/test-cluster.R
8abfccf99598504f469f6af88ce51c44 *tests/testthat/test-combine.R
959ec17317f4790b8c2e2af5c8818a32 *tests/testthat/test-cons.R
c72a8e0af0e25c2b79366c034ec0be10 *tests/testthat/test-detail.R
a47b2047ff7cbc0fa9041d6a141bd409 *tests/testthat/test-empirical.R
b574d23eff8195fbf6cff1cad58688e5 *tests/testthat/test-exprs.R
1bd721d4788cc73d6b8d2c3a86b59686 *tests/testthat/test-extract.R
5bd626567871cc9c1b2c86a1e71783d2 *tests/testthat/test-filter.R
3e626421ada945349a24cec4e4eaed7d *tests/testthat/test-int_extract.R
c401dafe4cb2e40263335a1eaed2736c *tests/testthat/test-int_input.R
db61af0f66bc998ab23c9f710d7cab53 *tests/testthat/test-int_output.R
816c597b62f8719be0f7268f6474234a *tests/testthat/test-int_resize.R
5bc85f5aa0bf0597557b76540da731e6 *tests/testthat/test-maxima.R
b1095bcc20029e656e83f71ec8d6c847 *tests/testthat/test-merge.R
6566d675432f9630c276d6992645e48d *tests/testthat/test-minimal.R
fba89789508134439a108560aea15561 *tests/testthat/test-mixed.R
4c661bf7ce664c88dc1a38888d70c64f *tests/testthat/test-norm.R
1db94e533d7e9cbba7b35c8470a9ed5e *tests/testthat/test-overlap.R
a54c6f2e3aae2689ae4f60d327d6d971 *tests/testthat/test-param.R
87feebd94944180bd57c1deea037b7e4 *tests/testthat/test-pet.R
a538718da9fb4db0720f6352fa12ba08 *tests/testthat/test-profile.R
a21bfe39d0057915e17a4e2aac2249c3 *tests/testthat/test-region.R
f619ebd41fa74cd483f2480d8dbdd107 *tests/testthat/test-window.R
b2874295a45a00b0d172d51b99f5892d *tests/testthat/test-wrappers.R
b37dbf8b2a3902a6460e49c50edefef5 *vignettes/csaw.Rmd
