d207e3e77f73390142f674c9e70ffe31 *CITATION
7f88266cf1f5badf552e097267473632 *DESCRIPTION
b7dcae4fa201ed2ea4760f81a2ba7cfc *INDEX
4f2eca02ed5eccf20ad8c168d38f505e *Meta/Rd.rds
30504c0cb0a2cee560db0616400282ce *Meta/data.rds
7f532e677b399de99b8ca9453103405a *Meta/features.rds
fcbb22131d98a8ccf64b0988a17a5566 *Meta/hsearch.rds
35d9d23902d5021406c086a0b1939c75 *Meta/links.rds
ebb38330f5a4e152d84c8a3b7044b718 *Meta/nsInfo.rds
45f0652d22623dd336724be1a65af911 *Meta/package.rds
1d85313bc3a5bc8b74d4ee3f93649d13 *Meta/vignette.rds
eed15029417221e8edf3fb5585ef3471 *NAMESPACE
22560224246cf70f77e2082c5e637035 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/PureCN
4a60d4fea100e027f1697023924a9b04 *R/PureCN.rdb
fc1bc70747286b18d155de204f44918e *R/PureCN.rdx
c0a1abec0c9afac63f2d710015c543f1 *data/centromeres.rda
3238088335c6c2d408cc8de2494d6289 *data/purecn.example.output.rda
407b9ec2af8821e1ff9e0b090ac41272 *doc/PureCN.R
1171a68099ba259175f325266c2810ef *doc/PureCN.Rnw
9ed5b23a43af0f25d517a013a4756372 *doc/PureCN.pdf
1ae545918c436da92f18105464b0c593 *doc/Quick.R
e445a24f1d5a97904a1289dbd8134e11 *doc/Quick.Rnw
68e70c8a05eb7123b8fbcc4fb77a426e *doc/Quick.pdf
51a2335a5fe463776b4078e8a48c344a *doc/index.html
13bbdb261054aa613cb6cce3a5ee3683 *extdata/Coverage.R
b2b72bd687efe407a18714b211e167e5 *extdata/Dx.R
a32b14bc419a5c61274fcd1c3d2da2f4 *extdata/FilterCallableLoci.R
e92af2f89c8d0de186246019d182ab34 *extdata/IntervalFile.R
ae31ff82c97f5cd07bbc424e124b5de0 *extdata/NormalDB.R
bffa05ecbd6672d0a12acefa73ba6250 *extdata/PureCN.R
3e55f3cbacf0ade2c2a406f1ad3f51b7 *extdata/downloadCentromeres.R
7df758adaaf5b6d487ac22e4dba6c31e *extdata/ex1.bam
1888862b9d22ddb8ca663eabc41c78f0 *extdata/ex1.bam.bai
7ff3a77a583973ad739082fc7d327298 *extdata/ex1_gcgene.txt
3cde10782966a832047779d3d1294e46 *extdata/ex1_intervals.txt
3600e3733184b2cf5822b61d26114658 *extdata/ex2_intervals.bed
ff600751c668406cf7c32e7362ce3899 *extdata/ex2_intervals.txt
3182e4f35fef60cd6a0d9fdec742c79b *extdata/ex2_mappability.bed
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35fcb62fd46b593d1269e249174c30ff *extdata/ex2_reference.fa.fai
9b97a8416ce0918d993be657b41ef8b9 *extdata/ex3_intervals.bed
bad94524668ccd54248551b63caf6d41 *extdata/ex3_mappability.bed
559ee8cb44c6df4fe00696181ef07c60 *extdata/ex3_reference.fa
b9affa44c1486b4a1dfe8552bc60b25c *extdata/ex3_reference.fa.fai
9242303d61055871f27ea41c01c1db36 *extdata/example_callable.bed.gz
3b1ed770f9de08a67d73e260b6bc97af *extdata/example_cosmic.vcf.gz
cb4501c1bb40ad0b7af797f7a756d74e *extdata/example_cosmic.vcf.gz.tbi
04ed9c18809a807d427a5867ff56533c *extdata/example_gc.gene.file.txt
5a11707c233e91086d895735bd7e7ced *extdata/example_gc.gene.file2.txt
78d8aca0fe4427f63b85c6fdc3d9bdb6 *extdata/example_normal.list
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3b6c3ae906b6dd7c11f67e1713232926 *extdata/example_normal2.txt
15d982eb620d8f5cdf671c75d96b745d *extdata/example_normal3.cnn
9f8f7691886d943ef1e0e70ca00cabf0 *extdata/example_normal4.cnr
bb5da3767dabbd7a51ae717fddfef7d4 *extdata/example_seg.txt
79937e90092e791bd91c7a045bd921e9 *extdata/example_tumor.txt
5d73baed8fb0ff5dad0a4bb2d55ef1a4 *extdata/example_vcf.vcf
edf609a37d88244a6c43b8d7a4e86c27 *extdata/normalpanel.vcf.gz
d9676085e3af0a6e9847bf329e96e1be *extdata/normalpanel.vcf.gz.tbi
efc17f1901c0090230be09f42bd24366 *extdata/test_coverage_overlapping_intervals.txt
44afac3181188a9deb246f94c0bb5147 *help/AnIndex
995ae8640b90cee9dd4ed05524743bd5 *help/PureCN.rdb
00af1abf230488600915405899d92970 *help/PureCN.rdx
e954f84371e919a75eaaf110a8d80f25 *help/aliases.rds
c82572651a014e50b243750932cef1ad *help/paths.rds
5be7c1117d50a8ccbb2ba149125241a5 *html/00Index.html
622e87d7a6bbfae144f9cfdfe38151c0 *html/PureCN-defunct.html
5b3911ae6681ca3ca5611b0e025b5838 *html/PureCN-deprecated.html
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dc8035ba6cbaf20eaee5c9d185bbb67d *html/annotateTargets.html
affa9f62130a6d33b6357867ed419831 *html/autoCurateResults.html
e5ba23d35b972017829a4000433a0a2c *html/bootstrapResults.html
09418023e9f37b4e34c7682115512e15 *html/calculateBamCoverageByInterval.html
f7b7a8e29534a8b950e95609028fc7b0 *html/calculateGCContentByInterval.html
1f2ca5d18ea4abb85ff3f382f70dce3b *html/calculateLogRatio.html
bc3461ff91d066b558c2a88e90776c90 *html/calculatePowerDetectSomatic.html
5f1b4b51d5faffaafc9b92dfbad35935 *html/callAlterations.html
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2b37db82023770df4e3513021d334faa *html/callMutationBurden.html
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9c1a76143e5929be9ef5f04f3350956d *html/createCurationFile.html
7cd9b8c76d0bbeb4a1fd86c8c81d6e45 *html/createNormalDatabase.html
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61ee133739cac856bc95b495a7aed90e *html/createTargetWeights.html
06ffb13b91253c4329f993ddd2b9ff75 *html/filterTargets.html
2781ecf277cb30572a73698824b49614 *html/filterVcfBasic.html
94b0fefc0774a7fa7d7f4e1e72f21719 *html/filterVcfMuTect.html
6b8f8dfceb0a44178fc254dcad7dae9e *html/filterVcfMuTect2.html
4bd57c346b1eafc59cef16da5bb255cb *html/findBestNormal.html
c34ea935f267173e189d2ec6999c56ad *html/findFocal.html
30a0b20e7a94698fabf1ea4c75a82db4 *html/getDiploid.html
9aae302e64b0d0384d343d7421851d95 *html/getSexFromCoverage.html
a2d16a87682df91c55bc2146aa8054bf *html/getSexFromVcf.html
b31c1328b42c03a2a8c76e13b6960d51 *html/plotAbs.html
8ed8c74adaf698e938bd385a28162f06 *html/plotBestNormal.html
adf81664ed80aeff21d696edcde6b60d *html/poolCoverage.html
43bf3bb3e390d2688e95a2fdc41d435c *html/predictSomatic.html
2c32748b0ab5c62c2add8f5e85b69846 *html/purecn.example.output.html
daaf955bea8d527f4445ab7345528f65 *html/readCoverageFile.html
32696a3c80ce619816f64e81c8947514 *html/readCoverageGatk.html
ccf03abb3245328ac67424c5d5fa8382 *html/readCurationFile.html
3fba8d9c76cd2af0eaf473a6df6a57a8 *html/runAbsoluteCN.html
b22d5bd1093fff3617bd23cf85388b72 *html/segmentationCBS.html
fd05a71d0e66c0e22ffd3130563f43a9 *html/segmentationPSCBS.html
1a30e2c980b43d6467a889fe7ba1a579 *html/setMappingBiasVcf.html
11684921c14522756e6745aee74ca0f7 *html/setPriorVcf.html
9af9bdfbee1d64e80e37f22dd41702a3 *unitTests/test_annotateTargets.R
c84963bf3235ff7ca648e93d71610999 *unitTests/test_bootstrapResults.R
8377c40118606aa8d1cdc758d9cb2593 *unitTests/test_calculateBamCoverageByInterval.R
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a3e6cd33fa682823d92810e840ce4a96 *unitTests/test_createCurationFile.R
921131f4de53a004d34038353aeefd20 *unitTests/test_createNormalDatabase.R
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c3eb971e1ba71a222d39932fab6b64cd *unitTests/test_getSexFromCoverage.R
255ee68eb5c90a68608d0455328e2e5a *unitTests/test_getSexFromVcf.R
60be062342447dba0678b01b491f57b2 *unitTests/test_poolCoverage.R
dbe751ac232c0c5b941e5236bd3b44f2 *unitTests/test_predictSomatic.R
e9608821e07d1af0c44a49336814d42a *unitTests/test_readCoverageFile.R
0ed32bc2cdfd014cfe6c442832db8673 *unitTests/test_runAbsoluteCN.R
1e90b12f272c6de1100e2f1aaa226e83 *unitTests/test_setMappingBiasVcf.R
96ca0d2e680ba59f973f402337e74286 *unitTests/test_setPriorVcf.R
