94bf0121c6a20d29f930b871a4f92eda *CITATION
b27a7facf568e11022762078048586fa *DESCRIPTION
68bb9ab215ae4b272ec27b23211bae93 *INDEX
bb087882b665fe8e24160a58aedd00ce *LICENSE
cc8b7f360141bcd636437e2fe8985e93 *Meta/Rd.rds
aadc0b435cd1ab6789777981948a0c5a *Meta/data.rds
1d15b8cd6573641f81c4126b0438e9c2 *Meta/features.rds
6e1110579b264a70272b313efe08b119 *Meta/hsearch.rds
e1bfd9c76e59caa4575b2a21dc44ecce *Meta/links.rds
433b207b4a68d60efdfb225c10f4f93d *Meta/nsInfo.rds
cfc7064a194f1919ccf5ed9027b71894 *Meta/package.rds
d97cb4a501e891179430d5dbfb65ccb4 *Meta/vignette.rds
529d6739f5d3e673afc9a295d7862ebe *NAMESPACE
fad59674387f98c24c21f8f0359c6381 *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/CNEr
52f784a6262ca7aa826bde0fcd1ecee6 *R/CNEr.rdb
dfeb4a908c3d9fd9d8e8e9a57528700e *R/CNEr.rdx
a595fc03c3b3d57f048c4e21a18c7cd2 *data/CNEDanRer10Hg38.rda
85fca72fe185084dbb12393bbb56c94d *data/CNEHg38DanRer10.rda
d7aff5e8ce701e2ce81feb5ba8434b73 *data/axisTrack.rda
05e4a1691e623dbc5d5132c625c3e952 *data/cneFinalListDanRer10Hg38.rda
3e2c63d5839dce07a3f8a017924633e6 *data/cpgIslands.rda
f636989efeff6b5effb53b546919718f *data/grangesPairsForDotplot.rda
fb9424ea5abd0f82ef1105e8462b8a1a *data/refGenes.rda
25985dd540127241e49d7c68285d3e39 *doc/CNEr.R
2de5bf342921f97286a553613e6aa05b *doc/CNEr.Rmd
7fc3a317f5e14f06d693a3175ca2669b *doc/CNEr.html
d2a39537337b794555e027298999ab96 *doc/PairwiseWholeGenomeAlignment.R
757ca2f473ff91bd78bd8cef0d315e38 *doc/PairwiseWholeGenomeAlignment.Rmd
9f4f6f3e237d03d7016e0cdc9831b885 *doc/PairwiseWholeGenomeAlignment.html
5fe54fa153d8ed86ace9301a0b2b7d82 *doc/index.html
e1225e2387a670279ab8e2f5695a5b62 *extdata/chr4.hg19.galGal3.net.axt.gz
9c8c4347211a68e2d2bdca8b3eb2a995 *extdata/cne2wBf_AstMex102_danRer10_48_50
144c4e621b5903d66fce90d40ff3452a *extdata/cne2wBf_cteIde1_danRer10_100_100
703b7fae3bd724a255a201e07f0f19ff *extdata/cne2wBf_cypCar1_danRer10_100_100
aad28bc8c6f7865a28ec3b4c06aa7517 *extdata/cne2wBf_danRer10_hg38_45_50
ee3f3bafa1ea2dd69057da90d4df026a *extdata/danRer10.hg38.net.axt
f0c8e5aa59cfa775c42fa54300a7e108 *extdata/danRer10CNE.sqlite
32f9e6948d016e9935633c6f1c34ed43 *extdata/filter_regions.danRer10.bed
8f357f770b042ed678b4f2b38e687053 *extdata/filter_regions.hg38.bed
83a080592fbc9a9e1e3c8045874bc4b6 *extdata/hg38.danRer10.net.axt
109773cc892befc7f16e64051a2f3180 *extdata/rmsk.fa
ecfff71e276939f8799b675c0035c131 *help/AnIndex
6d6153f3a0b8beba47d7074f1db32ad1 *help/CNEr.rdb
7d716d364095057b2b13821f73d60eae *help/CNEr.rdx
5e97a6382c0d7593f9eaaf2252927a17 *help/aliases.rds
09207a46f2a6c8a20fe3736e3a937f94 *help/paths.rds
0146ecff14185cecc7dee67137fc59af *html/00Index.html
71b7c9459958b9b25e0ee946fe35c9b0 *html/AssemblyStats.html
40353f97abb50a4118128dbc6f2544ef *html/Axt-class.html
94fd07ba102624a6d6f5de51943d3b8f *html/Axt-util.html
ce9fa62bc5ecab3cb50176c60d3f0b70 *html/CNE-class.html
51b5dfa892091c249bb3372804752b39 *html/CNEDanRer10Hg38.html
3e8dfa52dc4ca781a6eebfc182af3d35 *html/CNEDensity.html
a8d84f52b469cc580bb061cdd2e9ea23 *html/GRangePairs-class.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
4108373a2e6cbe8326abc72bdbf4b87e *html/addAncestorGO.html
fcb23b897a79dee8ecca1da764c118f9 *html/axisTrack.html
a0d7a4411217725a643491e14a06fcb3 *html/axtChain.html
bbee4884a88f592759f6253efea25325 *html/axtInfo.html
34213fad0d7213dbb657183995fcd16b *html/binner.html
3500850c1b3ddfcdcca282ee54c5108b *html/blatCNE.html
aa9cc1d45de3416ed0e0bf58e7460208 *html/ceScan-methods.html
2cfd1aa75e52eb95491fb8ac3d203057 *html/chainMergeSort.html
5920b540edf8892fa426dba888dab672 *html/chainNetSyntenic.html
628d974e4d9c7fefda1fc60cf8c73d82 *html/chainPreNet.html
810ab247804b329da4dd402c6ba8e441 *html/cneFinalListDanRer10Hg38.html
884e2f8952f2a4f8d9e660feca660829 *html/cneMerge.html
5489a6018621b853bf536e7d8eb91024 *html/fetchChromSizes.html
46cb00c8fb3e69e7a8ba315188261b98 *html/fixCoordinates.html
b8f3be52519196298f505667f89b0a0e *html/grangesPairsForDotplot.html
e68014430cc14f0ea1e6bc1d1576b758 *html/last.html
c359d1ea27479ba12e6128b5e5413f72 *html/lastz.html
6825f5afc0c892da8074da12c0a5ff4f *html/lavToPsl.html
0067f438233414556fe0d4b3505b1bb9 *html/makeAncoraFiles.html
3d6d621205b1c86818db7b7661345e51 *html/makeAxtTracks.html
1538514cccc73aa94eea1eda17bbc75b *html/makeCNEDensity.html
6ca5328b97bed45656d7f86a8f185a31 *html/makeGRBs.html
e97adaf690f1e1215f880da8c625a1d6 *html/matchDistribution.html
e86fb0c8f57d7675d4d9bdb73e0c5a01 *html/netToAxt.html
bf736fa3c9f6d275c0283da6d4a3f436 *html/orgKEGGIds2EntrezIDs.html
fe859ab2ca9c08d159b9c94b296bd8be *html/plotCNEDistribution.html
973f5a86f43f856bb84a01dbd098d09e *html/plotCNEWidth.html
047000ab6a9d15d4e66795920cec5d84 *html/psubAxt.html
1ca9b83406a83d2ddd91d0ae8f93d15f *html/queryCNEData.html
aa2e92f2ee66f5f12f3ab28f122f3a8c *html/read.rmMask.GRanges.html
f40765cf7d03145c797b3d86352585be *html/read.rmskFasta.html
c8c0810dea558ae0fcdda937b9a0102b *html/readAncora.html
50646c48aaa7d25cc5963218ab0921b5 *html/readAncoraIntoSQLite.html
efc1915dbd4f686ff9c0f67bbb1fe1a0 *html/readAxt.html
f9aa2124ae0c247d17da2aa15799b729 *html/readBed.html
69cb8e80a7cf7aaccc16a698c7161a98 *html/readCNERangesFromSQLite.html
2b9013f4f0eafc903aedc2f8a5c40bc5 *html/reverseCigar.html
d67e040fbc7566396ee2fc8063944bcd *html/saveCNEToSQLite.html
25c9da3e92a4c6fffd5e9675ca9559e5 *html/scoringMatrix.html
8b57530e5e21739e5ba78561c0972895 *html/subAxt-methods.html
9ab7a7f33287351ea00f89fdb856a8fd *html/syntenicDotplot.html
52b97952d4a3ff3595186527ed7d8bd6 *html/writeAxt.html
998463bd79562262d55be2a3f139e946 *libs/i386/CNEr.dll
a32ee9d2808067ed7532fc72df9543a3 *libs/x64/CNEr.dll
ec85324af0f35f446e7f94ec7477fd3c *obsolete/CNEr.Rnw
6922454ebccccaa223412f1e90952a48 *obsolete/alignment.c
3b502ef13330de1cd98dc4288a6f43d1 *obsolete/ceScan.r
d14cd8fb9911e5da6a2ba93af6d5974a *obsolete/ceScanR.r
0b52e0839eedfa011db6788f30472403 *obsolete/class.r
cdd26c6f3a003ce2e80db8921c7a7857 *obsolete/src/ceScan.c
b9b504316a8eeb190646972e165f979f *obsolete/src/ceScanBranch1.c
ed4391ac6a30aa3da32d63d7cbf5b17a *obsolete/src/ceScanBranch2.c
0a1fe70559c587a9104001f5203af75d *obsolete/src/compile
9e3c821c3f64ccfe466aa466d5f82ec5 *scripts/danRer10Pipeline.R
5f67d785a452ecc6f8168088a7b8b0c9 *scripts/prepareData.R
