e36783f1bf3e5a47b837f64ea56aa67f *DESCRIPTION
c377af424b4a4a4f18555630c03eb057 *NAMESPACE
00b6123963a330a931936f7d7e49540b *R/annotatePairs.R
ab541e46d1dc1c93ed9e80aff4b7997a *R/basefun.R
1e4e88f95a1b2d63303565c23bd6e3be *R/boxPairs.R
a1cfdb94dfbd6f17c75b16db7739021d *R/clusterPairs.R
94bfa56fe7dc9bcb67dc576c382d6abc *R/compartmentalize.R
3c41ec5e3037bb4cbb2c305ab338dd1b *R/connectCounts.R
67224df85737d95d4de1b5a0fdd0f521 *R/consolidatePairs.R
57da27a9b4e2c263ed0744e6f3db1ebf *R/correctedContact.R
7a15234b6107a70817a111cefd05dd18 *R/cutGenome.R
f6fb6e3ef2dfd7cda3f89c344f1dabd4 *R/diClusters.R
ad539453bc660a3f6a8f2fb343976080 *R/diffHicUsersGuide.R
6c4fcbf5c67b2665b2ea6bf33816dac8 *R/domainDirections.R
a7ba2a602506414ec66f726df43581d5 *R/enrichedPairs.R
39f34d7edf74614cdffcebed2f8c4602 *R/extractPatch.R
916689f12fa5c92f624c18af685843f2 *R/filterPeaks.R
4dffb79884794e95d6435561d4186161 *R/filters.R
cd677027734fcc2cf6126934731fd71b *R/getArea.R
5a3dfc50c5c6785cf69929a116f90f8e *R/getPairData.R
cac1a06c120df16855e4992122f5a97f *R/h5utils.R
c09f285841868999438e1d78d78dba3e *R/marginCounts.R
55cf2acb62b1cd236c9addb1cefd6783 *R/mergeCMs.R
82d078f22dfbc00f1fd8bfeeaa143678 *R/mergePairs.R
d1046bee2ae192e50249e21f79fdd999 *R/neighborCounts.R
34188723a5e41035036a772d7d9a90cd *R/normalizeCNV.R
df2aabe67fb7eae79486a22226fb39d2 *R/pairParam.R
87e27c75aedb7b35a1759b1c41716432 *R/plotPlaid.R
360b50e2433543f249169a5403849d36 *R/preloader.R
700ef1850155930a8a9e80060c7674eb *R/prepPseudoPairs.R
56e68dabd6d8fd18676be195d15cf38b *R/preparePairs.R
e3489789ad95009b40096b582e061cce *R/prunePairs.R
fcf859870c72de07a451b94a37a93b7b *R/readMTX2IntSet.R
fecdc8938ca5151e07fa147913d11b78 *R/rotPlaid.R
e242989e9ae6d5db88f1adbf28ac3350 *R/savePairs.R
dc58d6e15ee1e7ec12bd65313457ec43 *R/squareCounts.R
26de068bf9206134daefc5b51b3d7868 *R/totalCounts.R
c540460647e0c50ffe6fab9e394fa902 *R/weightedFDR.R
caecc766734f5321a502d9fdd9a02cd4 *README.md
6ea044f1e40d598df72a95e408b8624d *build/vignette.rds
f5009b0cc7fcb0b14eec0aada5fb85f0 *inst/CITATION
79064ed32e48ac2f74536eecf47ef758 *inst/NEWS.Rd
ec6af85435a225068580de41f121f7ef *inst/doc/diffHic.Rnw
77d83a06e6b29e3c3334b33db81af4a3 *inst/doc/diffHic.pdf
eab21f66d5334ae64eb525316a264f86 *inst/doc/diffHicUsersGuide.pdf
1eb4acfa59ffe49b9a1754f0114f23ad *inst/exdata/cuts.rds
beece61b4f038a89e2c1e7c01d1602ef *inst/exdata/generator.R
3bc4511ce1aab325d07a2f152d2158f6 *inst/exdata/hic_sort.bam
2e668d0500a9863b1cadfcc1063891a0 *inst/python/iter_map.py
bf40eb3117433f4ab9ed45c703a801e1 *inst/python/presplit_map.py
c7902ad6c0e56849a55ba3f34b2b54b1 *inst/tests/run_all_tests.sh
baa12fa5da66ca67440d85b0f9ae0574 *inst/tests/simcounts.R
3a2f6bb068c66c4eeabf10287512f7cb *inst/tests/simsam.R
181c5ae072da82a083a159a1d62655e3 *inst/tests/test-anno.R
b5a7a51e1f0f729d10188050e2c5579a *inst/tests/test-anno.Rout.save
d24727aef721455ed397d2046829403f *inst/tests/test-box.R
5dde208fcd13a8794acdd10d238cdc3a *inst/tests/test-box.Rout.save
4912d28e79b64507d722849195900510 *inst/tests/test-cluster.R
637122896a0fa4c557806187847f578a *inst/tests/test-cluster.Rout.save
5ceed070793c04989a57b29c8455ee1b *inst/tests/test-cmmerge.R
c0a341ca79eb3f61f49927f31b22880c *inst/tests/test-cmmerge.Rout.save
1fdd3bf747879aa68eb83357cc8185bc *inst/tests/test-connect.R
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ff401bf04feeaf85b3200a00e596445f *inst/tests/test-cut.Rout.save
92ade1257a03b74c0382a9f558d7b19c *inst/tests/test-diclust.R
ab1a56f41f234a7ed2bf9ceeb37b634b *inst/tests/test-diclust.Rout.save
7152bfb0c86ffd7c1b55af0b7d50b126 *inst/tests/test-dnase.R
c0ec034fc07b7894629e88dffd0df924 *inst/tests/test-dnase.Rout.save
6552cf00ff881c821420117bdeabe3f3 *inst/tests/test-domains.R
0ef4072ae88653d24862380d15f2d863 *inst/tests/test-domains.Rout.save
eb7b17544351f8996e01fd145a59c944 *inst/tests/test-empty.R
8d8ff8e159eec86c3bbb62e7700ec351 *inst/tests/test-empty.Rout.save
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3c2899fa5dee0e63934850a5d55b3b76 *inst/tests/test-hic-pair.R
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9fee4099e256c476181da8441dd1fbda *inst/tests/test-interactions.R
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aac54b09efcc53b0d32e7c694419d468 *inst/tests/test-itercor.R
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6ad23686a8a9956e53553858015b424f *inst/tests/test-margin.R
1d367309cec8b40f9cc21be093f88432 *inst/tests/test-margin.Rout.save
f7cd38d5d68f8050792b240b38c4c222 *inst/tests/test-neighbor.R
7dda21c95cd1f42a0fa7689803a19c56 *inst/tests/test-neighbor.Rout.save
f65352d5900f2b8adffea99250a097ac *inst/tests/test-pair-manip.R
31027a67d617e66f3c2c2677d47f14fd *inst/tests/test-pair-manip.Rout.save
f6cb88db2ac54f5f3fa946dec83025bc *inst/tests/test-patch.R
9cc9b3f3f603a90a71f7f97e7c4e0a2f *inst/tests/test-patch.Rout.save
52af1d2fd21f17a8d46b6f1552cfafa8 *inst/tests/test-prune.R
5c86d72a6d35f0c4b844ade844837ed3 *inst/tests/test-prune.Rout.save
0dee0efd21199b5d44a4fe5051162562 *man/DNaseHiC.Rd
c58319f8c6388caff1b48657ad9b661c *man/annotatePairs.Rd
3f3be943996ef48cea73aa9051165bed *man/boxPairs.Rd
8c766d6ae95df04cdf907e5be5407b61 *man/clusterPairs.Rd
c720009b392586d32e66780886e382c5 *man/compartmentalize.Rd
aec0f3b1560856b6057bd92d3839648f *man/connectCounts.Rd
2234802a2ae489b40de0f59ab7781351 *man/consolidatePairs.Rd
da74a80e41b77d85d5f876f611df16a8 *man/correctedContact.Rd
442766abeb9486a2906adebf9a16d6f6 *man/cutGenome.Rd
e339380de8202272a0e48a5afb304e3b *man/diClusters.Rd
b275ac6c30ffcbe9fd245a02d97de45a *man/diffHicUsersGuide.Rd
56ffd8e2d94a08ac2aa75d6258553c23 *man/domainDirections.Rd
4fde1f5a18d6a2cafec3a4446bd196b9 *man/enrichedPairs.Rd
92f91868d3b736675aea1ed6e2dd1d19 *man/extractPatch.Rd
0db0205b64695ac76d9f040d5a21a9a0 *man/filterDiag.Rd
81ef76e1e644f6368c49cb0cfe12e647 *man/filterPeaks.Rd
46bb7028d9d6b46d0bf5c252db89e5ea *man/filters.Rd
af438a678d3ecf09490de24e8c681851 *man/getArea.Rd
1ade223cc1f179d4accfdd4e918c732c *man/getPairData.Rd
9345e2bc71d237c6fa376c7929ea991d *man/loadData.Rd
52c6bf340513448ae97f49cb27c9b0f0 *man/marginCounts.Rd
0c6d637fec50f1466355698554b340c3 *man/mergeCMs.Rd
d09414040261d71171d5b468677d32f5 *man/mergePairs.Rd
ff4768b42696ebfe2e31b88b73a3062c *man/neighborCounts.Rd
f9a5627a385fa7975ab82ad3095ea0dd *man/normalizeCNV.Rd
2b742ddbe505ba81faa493ee031a17cb *man/pairParam.Rd
28484d65b43f4ca414c177bb4200700a *man/plotDI.Rd
8c055f6fbb21522e381cf65eb259ab67 *man/plotPlaid.Rd
732a5d26eba7ddccbcd8758629a0f2ec *man/preparePairs.Rd
1099189812259c1077c54a22722db5c8 *man/prunePairs.Rd
4a741a0dca753d9a568618b953128cf7 *man/readMTX2IntSet.Rd
adc8853ea7c4c23a3cdc5ea4886ac262 *man/savePairs.Rd
dcb054c1a927c71f745e5795321fdaef *man/squareCounts.Rd
436d1224c6951a403d1f4ccf9f830992 *man/totalCounts.Rd
7b8d1c2c8939e293615971dd97729f83 *src/Makevars
0686d1cfa1bd7eb6f54d1aa2683d17d1 *src/binner.cpp
5e014767f29cde9ec23bd6d231b7fb3d *src/check_input.cpp
09da6dfafc56e5aa1e6bb96008df374b *src/cluster_2d.cpp
60998a371ce9c27c16a10e208c23d262 *src/count_background.cpp
dfd53aad02c26b869fb5022d872f8f3b *src/count_connect.cpp
f56ff618fe83618c40986932b991c504 *src/count_patch.cpp
5dca3095df654dfe2f822ce6de9afdde *src/diffhic.h
44880d40d3fd1e9abfe5cfbb27a711a7 *src/directionality.cpp
8c8ed81b1ebe392f50ff3cee9550072e *src/init.cpp
deb091d057e85ff465dd386fb282a6d4 *src/iterative_correction.cpp
f5f98415110ad5b56c2ba5043fec7fa8 *src/neighbors.cpp
f0fec08c233ead8ca09c5a37dc22471e *src/neighbors.h
d9e05b3bceae3be249940a55c8966e7e *src/pair_stats.cpp
f07279df497a990eb8f49f98a2375f4c *src/quadrant_bg.cpp
ba41ad8693f4330721b17a29d4563632 *src/read_count.h
02f0fd408a8034d0c3b7818ae59e3e8d *src/report_hic_pairs.cpp
f2c0cae731f32cafaa8c82f206ce5d3e *src/trended_filter.cpp
c7024d67ae958ec730b0eca2e2b97027 *src/utils.cpp
e461aa025bb5cf026b7b8771b983b149 *src/utils.h
7700465af2c0cd6865a67c4c785568e3 *tests/test-basic.R
14535acc2a92cd0fa52d8c8f0ecf0e43 *tests/test-basic.Rout.save
74cbeee96f80dc99c969971a37c75a8d *tests/testthat.R
1b13443adb5de94f6d5d08cadcec6df6 *tests/testthat/test-cut.R
8c0074bf0dbbb53becafc2e3cfaedaf7 *tests/testthat/test-input.R
ec6af85435a225068580de41f121f7ef *vignettes/diffHic.Rnw
