51b532106ebc58487b5bb39b25065ca1 *DESCRIPTION
22e5cff817c0ffd15fd20d248f4bf6d4 *NAMESPACE
d14f09dcc1f694e8307905403aeb2329 *NEWS
54100462b257c87424a35e5cfe396c85 *R/characterToBSGenome.R
7ec7a2b63dc9be1cf1c97e4b6ba0d381 *R/circularRandomizeRegions.R
e24f1fa15a8c7a0c421f779b5f219ebb *R/commonRegions.R
a931956e9ad1c5e06ea4aa57ca5b4763 *R/createFunctionsList.R
4be38e3bcf58d1421b4f10f770f8773b *R/createRandomRegions.R
e30fbd54c94d4c457dd030ddc2978183 *R/emptyCacheRegioneR.R
f43df72afc03bf37ab907718f70f6231 *R/extendRegions.R
a333892587f50586589140c1275d7152 *R/filterChromosomes.R
070e3ff7089546532a51334b71fc8ed7 *R/getChromosomesByOrganism.R
a5a0e05e1f02ade5caf2d217b2150255 *R/getGenome.R
1d640f27d813ebc57f5dc4151e867c66 *R/getGenomeAndMask.R
a2ec5e879f2638b45afdb7ea9a4c3601 *R/getMask.R
226cbc65dd0a89cc14b76bc29cc85bfb *R/joinRegions.R
5102f18650dbd44925a01e33d1a0f9c7 *R/listChrTypes.R
5653eb47543ed8d91407e5c8672aa2e0 *R/localZScore.R
84c82092bd6ce53aa2b3033ca3664b93 *R/maskFromBSGenome.R
739068bce0867c8653699e6348c6d0bf *R/meanDistance.R
16933c775d5fc95eb9f65e7f8d6df208 *R/meanInRegions.R
972b8aef1fcb1228d0875c7b510aa197 *R/mergeRegions.R
d334e3b37cd35aae8244501ae970d411 *R/numOverlaps.R
003232532aeedaffdd88f53f4f130ad6 *R/overlapGraphicalSummary.R
bb3a4b860ea7a2e0ec5e0d1f996ad1bd *R/overlapPermTest.R
e7ea9c9761a9fb08410937131934c4f4 *R/overlapRegions.R
d941473ab72d55eaad6d6508b4df6379 *R/permTest.R
7e16067c795df8365418cde10bb7f232 *R/plot.localZScoreResults.R
2a00f18940ca2a22df1b2cf0799c9128 *R/plot.localZScoreResultsList.R
1179ff69b31095d4f1a62eacf21e1856 *R/plot.permTestResults.R
b7af43039aa8db6c74c8152b7c80f1f9 *R/plot.permTestResultsList.R
669986a19457129f027b7e9c0a4d184f *R/plotRegions.R
2751110699521ecb14eefd063d8fe73c *R/print.permTestResults.R
ec4a2cdfc54af04132df7a8c302efebb *R/randomizeRegions.R
c173424d84f935e4d492aad8a8d0bf48 *R/recomputePermTest.R
132d40c70fea4acc22d26e5e4eead507 *R/resampleGenome.R
c8311c87765584b753472111cc5240a8 *R/resampleRegions.R
f941e349fe097d63daec0b2a16012c4e *R/splitRegions.R
70094981f8c8f30c5c5b53af184306b1 *R/subtractRegions.R
577f5595d5366868c16d1285bb5a55e4 *R/summary.permTestResults.R
f87a4caa1d3c4c40ceea8ce6db3b5520 *R/summary.permTestResultsList.R
e016b6be4a8ab72b0200489b99318982 *R/toDataframe.R
ff1bc1188660376380ec38e2090e37d8 *R/toGRanges.R
8f133d24173627edffbd293cc34cb410 *R/uniqueRegions.R
5f9e762420dc7097f7221175fb525f10 *R/utils.R
4e64a1ee0073e0c478f982944d555d20 *build/vignette.rds
f676a926c485fed8e56803509d32f897 *inst/CITATION
8b8e5fffa2f589f08b62f7673640f3d9 *inst/doc/regioneR.R
b81d149c7343f0d084f9be44eef20faf *inst/doc/regioneR.Rmd
844addc38e2aad2a8c865423ff6ccbec *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
a41cfada535488a1e3d9b7cd2dd13ace *man/characterToBSGenome.Rd
be65c3c0acc24697965280e61fd360ef *man/circularRandomizeRegions.Rd
9bd0df64ac72abab5a95a91813cf8f44 *man/commonRegions.Rd
ed4daeafc6876fdb323e761c34a03eb9 *man/createFunctionsList.Rd
2a50c4239966f473093973b43027aed4 *man/createRandomRegions.Rd
d9645c4bbe90bfb7f6defdd79118a61d *man/emptyCacheRegioneR.Rd
42acb76422f71c06df0aa0e20dd44c47 *man/extendRegions.Rd
60166c1a1fe63b4ff9d3b62a94e32e51 *man/filterChromosomes.Rd
e22684175ed91bc04d736289f69a1005 *man/getChromosomesByOrganism.Rd
4cb5dce7c7b2fc2a730bac61c62043c9 *man/getGenome.Rd
d094992865188f5ef3c8620817cbd986 *man/getGenomeAndMask.Rd
935c5959aa7660c3c1e4f54abdd586a2 *man/getMask.Rd
19292945202ca993bf10fec6732ce0a8 *man/joinRegions.Rd
f5c1189a377799bfa644ed5dd2f29c0e *man/listChrTypes.Rd
97f4d067524371872e114540e9fed53c *man/localZScore.Rd
384bb77defe3099a84e245f6a86ca17c *man/maskFromBSGenome.Rd
5069cdd4cf8e91e844f0379904cfe93d *man/meanDistance.Rd
077b94aa280498b6d31fa02e74b5856d *man/meanInRegions.Rd
82231db70e283b2a3cb2acff37e1ca7f *man/mergeRegions.Rd
0d4cd031764d6ba44bb8b9e2c2b95f9b *man/numOverlaps.Rd
74e1eaa6d4ba4beba1cbebb8a618cbc3 *man/overlapGraphicalSummary.Rd
217fe4bc285cf5c8203955c9a1785550 *man/overlapPermTest.Rd
8d2f21178de70113f7c9a78a7ffe2a39 *man/overlapRegions.Rd
e4ca940913d9100dfa18c8f73689d0f7 *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
9d63c93f1d14da3c41951639bbd82755 *man/randomizeRegions.Rd
7788261c182e9d9ff5776b79de557b56 *man/recomputePermTest.Rd
76f220e0725e409e22051284a779e081 *man/resampleGenome.Rd
18c8b23b5c8a147e84a615de4136edcb *man/resampleRegions.Rd
0bfb42aa0230add1c4ef9c72a32d0dc9 *man/splitRegions.Rd
b73f5184c0ce3b9cc368c3894bd18232 *man/subtractRegions.Rd
06e29c404281e4e1450c7352ee7aa12f *man/summary.permTestResults.Rd
bf891eeadd11728966b4fcf2e50b3a04 *man/summary.permTestResultsList.Rd
7948bcdcadce1ae7b1bd33b3eca2bd06 *man/toDataframe.Rd
e4ce05d4f76bdae092e70af43d2fc367 *man/toGRanges.Rd
1ef7d4f3fdee7faee2c639628c3c4a24 *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
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test_numOverlaps.R
642896c379f21fb98826e941d630de8c *tests/testthat/test_permTest.R
84e29e0f4d4084abc7c64c068478a13f *tests/testthat/test_randomizationFunctions.R
3a528aa0847bcc16c3b8510aa8a3a017 *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
