9405c74e930e8a70b46e8a948e40f7f4 *CITATION
6a204587f634a0e9270b4fd705ebdfe6 *DESCRIPTION
46534afd6ecaa6fc2fadd843135f567a *INDEX
d53654765893d139c1ffb53a84da4254 *Meta/Rd.rds
8503e676975364d771072956cdbca633 *Meta/features.rds
612c78d5ce417d57b1cb3c98dcd84db6 *Meta/hsearch.rds
b43c75cc829d7bdfc93626fe596c42ba *Meta/links.rds
5501023819e29f4bc7e3021af7cab2c8 *Meta/nsInfo.rds
e6a7cd436c2fe015edd575cdd9f20508 *Meta/package.rds
645a00cfaad256d77c12a0914b0dbab1 *Meta/vignette.rds
91d6236d6dcf3c03e75ed33244c3b051 *NAMESPACE
9e7ee257475bd105d736bb682f015eb0 *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/girafe
8d78ce3194a8bde4f6e19a9a59cb5db8 *R/girafe.rdb
f35030dfb041e82a8ca3dddbacb7ae1e *R/girafe.rdx
1b858510fdfeaad73595e38ae899449d *doc/girafe.R
821615467d37c422daca738e4d725a67 *doc/girafe.Rnw
b75a6278aec450f478bd066093af04d9 *doc/girafe.pdf
4b6c989fd81ac587e07252a74b572e12 *doc/index.html
78bdd3cf1fe76f07d6d8794b36143b1a *extdata/aravinSRNA_23_no_adapter_excerpt_mm9_unmasked.bwtmap
45457d9387bcf968cb98158f4ecb7404 *extdata/aravinSRNA_23_plus_adapter_excerpt.fastq
30e276f3e8eb57e13e5584961a5f84a5 *extdata/mgi_gi.RData
985d76efd2a73765b05fbab767f6d394 *help/+5B+2CAlignedGenomeIntervals+2CANY+2CANY+2CANY-method.html
985d76efd2a73765b05fbab767f6d394 *help/+5B+2CAlignedGenomeIntervals+2CANY+2CANY-method.html
985d76efd2a73765b05fbab767f6d394 *help/AlignedGenomeIntervals-class.html
985d76efd2a73765b05fbab767f6d394 *help/AlignedGenomeIntervals.html
17509885fbf120c7295402d6666c016e *help/AnIndex
2fb159fdbf4951a9fb75b7df440e55fb *help/addNBSignificance.html
662b8933caeae7fce78da9bbe38e959d *help/agiFromBam.html
6ab88e265ca192d67666ee37e1df6163 *help/aliases.rds
550ff3df8b8bf1b45fda5cfe963e26ec *help/alongChromTicks.html
985d76efd2a73765b05fbab767f6d394 *help/c+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/c.AlignedGenomeIntervals.html
985d76efd2a73765b05fbab767f6d394 *help/chrlengths+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/chrlengths+3C-+2CAlignedGenomeIntervals+2Cnumeric-method.html
985d76efd2a73765b05fbab767f6d394 *help/chrlengths+3C-.html
985d76efd2a73765b05fbab767f6d394 *help/chrlengths.html
985d76efd2a73765b05fbab767f6d394 *help/chromosome+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/chromosome+2CGenome_intervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/clusters+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/clusters+2CGenome_intervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/coerce+2CAlignedRead+2CAlignedGenomeIntervals-method.html
5fbad5ba21203b8f737896a001653132 *help/countReadsAnnotated.html
985d76efd2a73765b05fbab767f6d394 *help/coverage+2CAlignedGenomeIntervals-method.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/coverageOneStrand.html
985d76efd2a73765b05fbab767f6d394 *help/detail+2CAlignedGenomeIntervals-method.html
2fb159fdbf4951a9fb75b7df440e55fb *help/estimateNBParams.html
985d76efd2a73765b05fbab767f6d394 *help/export+2CAlignedGenomeIntervals+2Ccharacter+2Ccharacter-method.html
985d76efd2a73765b05fbab767f6d394 *help/export+2CGenome_intervals+2Ccharacter+2CANY-method.html
985d76efd2a73765b05fbab767f6d394 *help/export.html
985d76efd2a73765b05fbab767f6d394 *help/extend+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/extend+2CGenome_intervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/extend+2CGenome_intervals_stranded-method.html
985d76efd2a73765b05fbab767f6d394 *help/extend.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/featureColors.html
24869fd21c4d4ff20f5164e42a6f1133 *help/fracOverlap.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/getChromLengths.html
d1078f9671bc22e60148fe906383fa14 *help/getFeatureCounts.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/getReadPosDf.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/girafe-internal.html
1cab57a881638d0843225e9fe86be673 *help/girafe.rdb
b25855f64f05ca0e6f812062945989bc *help/girafe.rdx
985d76efd2a73765b05fbab767f6d394 *help/hist+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/id+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/id+3C-+2CAlignedGenomeIntervals+2Ccharacter-method.html
985d76efd2a73765b05fbab767f6d394 *help/id+3C-.html
adf41e871b7b4e317449498781adee43 *help/intPhred.html
985d76efd2a73765b05fbab767f6d394 *help/interval_included+2CAlignedGenomeIntervals+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_included+2CAlignedGenomeIntervals+2CGenome_intervals_stranded-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_included+2CGenome_intervals_stranded+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_overlap+2CAlignedGenomeIntervals+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_overlap+2CAlignedGenomeIntervals+2CGenome_intervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_overlap+2CAlignedGenomeIntervals+2CGenome_intervals_stranded-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_overlap+2CGenome_intervals+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/interval_overlap+2CGenome_intervals_stranded+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/matches+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/matches+3C-+2CAlignedGenomeIntervals+2Cinteger-method.html
985d76efd2a73765b05fbab767f6d394 *help/matches+3C-.html
985d76efd2a73765b05fbab767f6d394 *help/matches.html
8c9edb30141e93031b85d59f23a99b2e *help/medianByPosition.html
985d76efd2a73765b05fbab767f6d394 *help/nchar+2CAlignedGenomeIntervals-method.html
2fb159fdbf4951a9fb75b7df440e55fb *help/negbinomsig.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/newVP.html
985d76efd2a73765b05fbab767f6d394 *help/organism+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/organism+3C-+2CAlignedGenomeIntervals+2Ccharacter-method.html
985d76efd2a73765b05fbab767f6d394 *help/organism+3C-+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/organism+3C-.html
985d76efd2a73765b05fbab767f6d394 *help/organism.html
3a5eb3dad5bbe85f71749f34c7148719 *help/paths.rds
eb636810a3444921af427009ad3da97e *help/perWindow.html
985d76efd2a73765b05fbab767f6d394 *help/plot+2CAlignedGenomeIntervals+2CANY-method.html
985d76efd2a73765b05fbab767f6d394 *help/plot+2CAlignedGenomeIntervals+2CGenome_intervals_stranded-method.html
985d76efd2a73765b05fbab767f6d394 *help/plot+2CAlignedGenomeIntervals+2Cmissing-method.html
985d76efd2a73765b05fbab767f6d394 *help/plot+2CAlignedGenomeIntervals-method.html
850d79ea2e1fd762c7d54ae9a56103a7 *help/plotAligned.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/plotAllChrom.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/plotAlongChromLegend.html
229beca3b778e65bf2c9d8d6931ef6d8 *help/plotNegBinomFit.html
6bb10cf35e0e9ab83684705f84bd357b *help/plotReads.html
985d76efd2a73765b05fbab767f6d394 *help/reads+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/reads+3C-+2CAlignedGenomeIntervals+2Ccharacter-method.html
985d76efd2a73765b05fbab767f6d394 *help/reads+3C-.html
985d76efd2a73765b05fbab767f6d394 *help/reads.html
985d76efd2a73765b05fbab767f6d394 *help/reduce+2CAlignedGenomeIntervals-method.html
56af3cd8d7c44bc335b96fd819fd9e36 *help/reduce+2CCompressedIRangesList-method.html
985d76efd2a73765b05fbab767f6d394 *help/reduce+2CGenome_intervals-method.html
56af3cd8d7c44bc335b96fd819fd9e36 *help/reduce+2CIRanges-method.html
56af3cd8d7c44bc335b96fd819fd9e36 *help/reduce+2CIntegerRanges-method.html
56af3cd8d7c44bc335b96fd819fd9e36 *help/reduce+2CIntegerRangesList-method.html
56af3cd8d7c44bc335b96fd819fd9e36 *help/reduce-extras.html
56af3cd8d7c44bc335b96fd819fd9e36 *help/reduce-methods.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/reduceOneEnd.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/reduceOneExact.html
985d76efd2a73765b05fbab767f6d394 *help/sample+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/score+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/score+3C-+2CAlignedGenomeIntervals+2Cnumeric-method.html
985d76efd2a73765b05fbab767f6d394 *help/score+3C-+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/score+3C-.html
985d76efd2a73765b05fbab767f6d394 *help/seqnames+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/seqnames.html
985d76efd2a73765b05fbab767f6d394 *help/show+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/sort+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/strand+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/strand+3C-+2CAlignedGenomeIntervals+2Cfactor-method.html
985d76efd2a73765b05fbab767f6d394 *help/strand+3C-+2CAlignedGenomeIntervals+2Cvector-method.html
985d76efd2a73765b05fbab767f6d394 *help/subset+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/subset.html
985d76efd2a73765b05fbab767f6d394 *help/summary+2CAlignedGenomeIntervals-method.html
985d76efd2a73765b05fbab767f6d394 *help/summary.html
08bbc5584a0966a7b8f1c611e0053292 *help/trimAdapter.html
176a136870c43368d7868e94136bb5c6 *help/weightedConsensusMatrix.html
4f96b3a003ff6c7931a298b5daac910c *help/whichNearestMethods.html
4f96b3a003ff6c7931a298b5daac910c *help/which_nearest+2CAlignedGenomeIntervals+2CGenome_intervals_stranded-method.html
4f96b3a003ff6c7931a298b5daac910c *help/which_nearest+2CGenome_intervals+2CGenome_intervals-method.html
4f96b3a003ff6c7931a298b5daac910c *help/which_nearest+2CGenome_intervals_stranded+2CGenome_intervals_stranded-method.html
4f96b3a003ff6c7931a298b5daac910c *help/which_nearest.html
985d76efd2a73765b05fbab767f6d394 *help/width+2CAlignedGenomeIntervals-method.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/windowCountAndGC.html
550ff3df8b8bf1b45fda5cfe963e26ec *help/writeExportData.html
ec9b0c47ee12379ed4de0e3a2f9287c3 *html/00Index.html
c89f1ea13a1636cf49af7794232f9b4c *html/AlignedGenomeIntervals-class.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
39f74613c62dffbee33507b28d90a8ea *html/agiFromBam.html
b3900bd314c77ae2f5f745b12d3721de *html/countReadsAnnotated.html
72288c5063c9523af8cfbccd7aa53a4a *html/fracOverlap.html
491bbaae7fa9d567ff86fc0e685aa2da *html/getFeatureCounts.html
bc24c49f85ff4615908c49ba883e315f *html/girafe-internal.html
a9085a1359125f4dccb969bbe0c2832b *html/intPhred.html
9918aa47fd8ca73c64a8802da84596ad *html/medianByPosition.html
47035f75119572703aadb316a4ce39da *html/negbinomsig.html
ae5e54058448cebb33be44924fd400e1 *html/perWindow.html
4ade609736d1182a2f65771c5008d164 *html/plotAligned.html
e64575d7093d85daa579379f829cb33c *html/plotReads.html
a80b4937cdb20c5513473bb658e81767 *html/plotnegbinomfit.html
4d6856ff61e30291164b5da481fdb72c *html/reduce-extras.html
0c1f0ffa39e3e75767d23975da23df10 *html/trimAdapter.html
3c02f0b027aaedba380984ccdf05a94f *html/weightedConsensusMatrix.html
1ed5a11dcbd335015437f237ac64d30b *html/whichNearestMethods.html
da6745800adb6f27977fc65e9d8819fd *libs/i386/girafe.dll
9dce83067f863149b4783c8d5bfc6c34 *libs/x64/girafe.dll
eaa62b132310d757d86f3bfabd4f18f3 *scripts/colourspace.R
7a293eb9a10d0b72220a8800d1638617 *scripts/prepareAnnotation.R
d9fd20e0cc7bdc5117b4fc63446d0f88 *scripts/readAlignedExtras.R
