cb11b82f80006bf424036372f4996635 *DESCRIPTION
ee545e2525ceb7f442933d42eb40d56b *NAMESPACE
d14f09dcc1f694e8307905403aeb2329 *NEWS
d79ffafd9dcdca1eff91a8b46ba41165 *R/characterToBSGenome.R
e86854c80677edda0e6ef2f03c6bc655 *R/circularRandomizeRegions.R
276421a174fe50940b0a9cafee72e2fa *R/commonRegions.R
a931956e9ad1c5e06ea4aa57ca5b4763 *R/createFunctionsList.R
ab2c273871d2e4e1a14db5b229fc6ba3 *R/createRandomRegions.R
e30fbd54c94d4c457dd030ddc2978183 *R/emptyCacheRegioneR.R
3b7c0a870807032e9998a28615135fd3 *R/extendRegions.R
095818385b5683c7072c3c33a0a19e8b *R/filterChromosomes.R
3fc717802455645a8f2250854b8449dc *R/getChromosomesByOrganism.R
f8e62dfd381207cdb89cf1fb76588fae *R/getGenome.R
62daad1eddac916906e1ae887dd25e2d *R/getGenomeAndMask.R
212c45a104c62a6125b82709082ea4b7 *R/getMask.R
de2e9036e0a60b83188c7d9f08701c04 *R/joinRegions.R
5102f18650dbd44925a01e33d1a0f9c7 *R/listChrTypes.R
8c1a23fd542a70f0147bb2fc7fb24fb4 *R/localZScore.R
45f1beab370f8421a8b061a2fd8aea36 *R/maskFromBSGenome.R
3c3116e12e652ff0bab95eafa5389a5c *R/meanDistance.R
dfff64442868a821620ad307c7debc13 *R/meanInRegions.R
7f652d27fabbdea25e1459e140c11213 *R/mergeRegions.R
9d47a30fca30a18c4769f64d76fc88c2 *R/numOverlaps.R
732f5163578cc84fab9ae9edb5de5c24 *R/overlapGraphicalSummary.R
72f2857616cc457ebc8468e9e7a681e0 *R/overlapPermTest.R
3dc9d1f9a32d0b2278ec96f7f6d448ae *R/overlapRegions.R
4480b29c16c755ec8a638dbb0f9839ba *R/permTest.R
212865022202bd4d53e867e92fa5c9b0 *R/plot.localZScoreResults.R
2a00f18940ca2a22df1b2cf0799c9128 *R/plot.localZScoreResultsList.R
a74a9cad9f7c76c76072e621b26bba03 *R/plot.permTestResults.R
b7af43039aa8db6c74c8152b7c80f1f9 *R/plot.permTestResultsList.R
2184e6363075a7d0ee26ca28d458e259 *R/plotRegions.R
2751110699521ecb14eefd063d8fe73c *R/print.permTestResults.R
392bddf7e99d1974a86442310d7e4690 *R/randomizeRegions.R
c0997e4f2e655bd4b771f5eac1cae3bf *R/recomputePermTest.R
1c71e9d97138c90f431952b3f10a4eea *R/resampleGenome.R
1ff9b8b0f27a97314d9a01862823a4fd *R/resampleRegions.R
9e4fb3e17abb552ec236606686b3ae44 *R/splitRegions.R
8b795d4d45d2595861b621031a3f6800 *R/subtractRegions.R
9e1a17b5309815a51841e2581f59f04b *R/summary.permTestResults.R
4d3a062c1d325c5a9aca54546fe0cad0 *R/summary.permTestResultsList.R
2c2b69e06477839e06c9b80b2abdf646 *R/toDataframe.R
bf3f213bd373dda04f795ed56f797f0d *R/toGRanges.R
b34c112875fdaedce50aa9235a2e1e7c *R/uniqueRegions.R
5f9e762420dc7097f7221175fb525f10 *R/utils.R
507bf16ce595d9ccfaad37af0ee6cd37 *build/vignette.rds
f676a926c485fed8e56803509d32f897 *inst/CITATION
8b8e5fffa2f589f08b62f7673640f3d9 *inst/doc/regioneR.R
b81d149c7343f0d084f9be44eef20faf *inst/doc/regioneR.Rmd
e4cb5fc43a357bd002e2a91952b0fe04 *inst/doc/regioneR.html
e14ae38851f2904cab155cc4a44549da *inst/extdata/all.genes.txt
da5d15cac75ba9ef2425e3190f9d7aaa *inst/extdata/my.altered.regions.txt
1930465a4dd42ebd5e20df3edb396a0d *inst/extdata/my.regular.genes.txt
ce631f7a842209a296e20cbfa03e0c93 *inst/extdata/my.special.genes.txt
a22f20b5a637c30380608ed24217f865 *man/characterToBSGenome.Rd
94e5ee4337c516db9676486453d8d6bb *man/circularRandomizeRegions.Rd
2842f531c68b75c2cddf64ea94d52e82 *man/commonRegions.Rd
ed4daeafc6876fdb323e761c34a03eb9 *man/createFunctionsList.Rd
c2f4d041af0c937fcd82dfa6a54a1420 *man/createRandomRegions.Rd
d9645c4bbe90bfb7f6defdd79118a61d *man/emptyCacheRegioneR.Rd
1d2e3476b16e0a433e142ebac7a5f474 *man/extendRegions.Rd
1810b60e4ecb4bc3486ee447a1863dfa *man/filterChromosomes.Rd
e22684175ed91bc04d736289f69a1005 *man/getChromosomesByOrganism.Rd
3decce313d7105bdebbdf6c83e0116c3 *man/getGenome.Rd
1ae0e9158f7b029f0405bb2e4d773cd7 *man/getGenomeAndMask.Rd
1459b57d1f035ca3c11fa8df6d251451 *man/getMask.Rd
861cad549b08b797ff4794201b997cb4 *man/joinRegions.Rd
f5c1189a377799bfa644ed5dd2f29c0e *man/listChrTypes.Rd
ff8ffc504878fd05a200d95171a67cca *man/localZScore.Rd
c3dbdaf207090ce52c96f70d283c5dd2 *man/maskFromBSGenome.Rd
a6ab34d62f7568bebb95942f7f455425 *man/meanDistance.Rd
c534996c799929c16036aad284370474 *man/meanInRegions.Rd
1e7dd946be45b2683faf40d59a8448ac *man/mergeRegions.Rd
4cbb0629dab0a12f39c8d0cc302ae6b9 *man/numOverlaps.Rd
0eefbeebb8d12c0d3d7a85fe4d92aa71 *man/overlapGraphicalSummary.Rd
397f509d7e45952a5aa29b7479c58800 *man/overlapPermTest.Rd
ad1bbb9f6c862d4811d790574f46e42b *man/overlapRegions.Rd
bc075b164f160d4541cc7eff2aafed49 *man/permTest.Rd
1a556a3e47fe31ee21adda5b322a9f5c *man/plot.localZScoreResults.Rd
9987c06caa33b32873e8afd0f3318846 *man/plot.localZScoreResultsList.Rd
d6526222518426881ce42bd60cd13cf1 *man/plot.permTestResults.Rd
11894e06b473b711b7e5a085c1b1f78e *man/plot.permTestResultsList.Rd
72002ee206ef5697fcb0566e02245e0c *man/plotRegions.Rd
bab20cdaf29ede2ab1b12bb63927e8ca *man/print.permTestResults.Rd
ed96abbf13b3c5a89f4204a10b652455 *man/randomizeRegions.Rd
7788261c182e9d9ff5776b79de557b56 *man/recomputePermTest.Rd
1f7ae239750b289f937d9cfc1cd4ac3a *man/resampleGenome.Rd
d9bfa33afed8d8a3896cd4806104c210 *man/resampleRegions.Rd
95a0fe65bd8712b73e17fcace6ae564c *man/splitRegions.Rd
dc4f4e584d210a966914ee68f1b4a45b *man/subtractRegions.Rd
06e29c404281e4e1450c7352ee7aa12f *man/summary.permTestResults.Rd
bf891eeadd11728966b4fcf2e50b3a04 *man/summary.permTestResultsList.Rd
48d30357967d304fa7856a7d4d04a0a0 *man/toDataframe.Rd
b2a511810596e00f4c4e9edc74d03bec *man/toGRanges.Rd
bd5f1ae25b6cd221092c305dd376cb84 *man/uniqueRegions.Rd
3437bfb0a3d066212117a460aec75d3f *tests/testthat.R
a2346e8c434da24efb9f2678944a89fe *tests/testthat/test_data_files/4columns.bed
a2346e8c434da24efb9f2678944a89fe *tests/testthat/test_data_files/4columns.txt
1f0c5da2d82d23b0c801382b460899d4 *tests/testthat/test_data_files/alt_sep1.txt
80b566a64bc16345ac30038d6ae68ab9 *tests/testthat/test_data_files/alt_sep2.txt
fa166f6e935088f22559fa352be76ede *tests/testthat/test_data_files/alt_sep2_with_other_seps.txt
dc2641b2d9c42681175dafbd37ff119b *tests/testthat/test_data_files/bed_with_header.bed
d24379285f9ba6791affbde1f3d84bd0 *tests/testthat/test_data_files/comments_and_header.txt
68b329da9893e34099c7d8ad5cb9c940 *tests/testthat/test_data_files/empty_file.txt
b12255c2adf3458668fab30473f53be3 *tests/testthat/test_data_files/noheader.txt
c57b45d971e6a8713b96867482fe1ed6 *tests/testthat/test_data_files/only_comments.txt
53aa852ce2f7452ec7189f1125b91e7f *tests/testthat/test_data_files/only_comments_and_header.txt
f138bede08bccdd03340548c561313f5 *tests/testthat/test_data_files/regs.bed
93af9789526d1fb3260ac734ab2ee68c *tests/testthat/test_data_files/regs.txt
fabc9db47c18a69476b735c210a1c19e *tests/testthat/test_data_files/two_valid_seps.txt
7bcd923f2f4ef31efcb8eef3fef9a6fd *tests/testthat/test_evaluationFunctions.R
b831856315f71fb1cdadd0db0ac7cec0 *tests/testthat/test_genomesAndMasks.R
c389a7c2ab88582be09a656cedda8f0a *tests/testthat/test_iteration.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test_numOverlaps.R
642896c379f21fb98826e941d630de8c *tests/testthat/test_permTest.R
84e29e0f4d4084abc7c64c068478a13f *tests/testthat/test_randomizationFunctions.R
715d073e3c0e8dc7ea46d8255b9beb70 *tests/testthat/test_resultClasses.R
26656efe65f6357316e3ae96a13f722f *tests/testthat/test_toGRanges.R
74eb4b0f1f75e26392f040692342b387 *vignettes/figures/Example1_fig1.pdf
151ee8917b149680bd6ad5173bc4bcd3 *vignettes/figures/Example1_fig1.png
2765b990b450cbe26c52e7a9dd8019e4 *vignettes/figures/Example2_fig1.pdf
eab9baf6d877cce19b55e8470c10e84e *vignettes/figures/Example2_fig1.png
39f1ed00f78c1eac91b430303a0ab5f9 *vignettes/figures/Example2_fig2.pdf
464aa6448adb2b99e5685f0964a23908 *vignettes/figures/Example2_fig2.png
f94cb2574236eec16e7bc57228bbd2c1 *vignettes/figures/Example2_fig3.pdf
28cf93af6e4a477e087918f4f4d6b350 *vignettes/figures/Example2_fig3.png
74fa9c83d5e3b40cc3b8a14c0c4a7f61 *vignettes/figures/Example2_fig4.pdf
d93da574b2a14574f95ef70d5a70263b *vignettes/figures/Example2_fig4.png
385f24453c4b7a9073fa2557adad5ba3 *vignettes/figures/mask_test_regioneR_small.pdf
e57573afef2bcb66b4746625af8f7a77 *vignettes/figures/mask_test_regioneR_small.png
3f1f240e9eb7ba862864674c425b74fe *vignettes/figures/regular_genes_5000perm.pdf
6c442fcd33d7e616b9b37fbf5a539fc3 *vignettes/figures/regular_genes_5000perm.png
c76d1e637edb3504760ef67b96fda613 *vignettes/figures/special_genes_5000perm.pdf
bad1dcd6097b0118576dd2c711af4af9 *vignettes/figures/special_genes_5000perm.png
ced2c4be4e4f3d67517a0dd59ea3fe60 *vignettes/figures/speed_test_regioneR_small.pdf
2162e6dc4948c40e8cfb2fa8d76770b2 *vignettes/figures/speed_test_regioneR_small.png
b81d149c7343f0d084f9be44eef20faf *vignettes/regioneR.Rmd
