5827bb0378bb6d9eba4f3b85679b405e *CITATION
ecbf2c2dc024d67716f03b69a5474a8f *DESCRIPTION
73f65997005ef4c649e574b86d97768f *INDEX
ca2e1f2da8d6d7e5c9c39dc916851fd1 *Meta/Rd.rds
cad5cf9dfdd9cc268960d2bc91a91f68 *Meta/data.rds
c8440c06be5e093e05779d74c0ffa6b7 *Meta/features.rds
c5a138c4a2c9b680d2210ee5d8bc0954 *Meta/hsearch.rds
543150e6fea707801a2016141bc3a1bc *Meta/links.rds
4c5e38226b3249ccb98750297a2c8337 *Meta/nsInfo.rds
020af2ff375a434158257e98389959e6 *Meta/package.rds
e40fc47c0e67c7a8695463846162b90d *Meta/vignette.rds
e46f3cc40021051b275d73664f95c325 *NAMESPACE
ff19d0f3d7b3627da6dd5d0eea0faf78 *NEWS.Rd
d6c68f1fe41ced6e98a766a3757313da *R/R453Plus1Toolbox
ab89aef574df3aec6ba77ac9081477c8 *R/R453Plus1Toolbox.rdb
3b1fdd66dbf880da3914a22028fa033a *R/R453Plus1Toolbox.rdx
489b186b7f6972a885de18c594e85909 *data/avaSetExample.RData
b26f9a4853b43a22c73387c7c6cd9eeb *data/avaSetFiltered.RData
c1d944b854d4b800e8a04419c164a882 *data/avaSetFiltered_annot.RData
00f66e479bf2a22e7c67895ac3e35c5e *data/breakpoints.RData
02867656f6aa4d42f525cbabd3bf17c8 *data/captureArray.RData
10ed97379a88bec5258cfc10e7c9e189 *data/mapperSetExample.RData
5a557fe7262c7119f90bcd5cb962011e *data/plotVariantsExample.RData
3c88567213bd1168398b7389670197a0 *doc/index.html
b2b1e50be8ebfd6d838f93709049a4ec *doc/vignette.R
be004f03830183f688e34c1f1180628f *doc/vignette.Rnw
b735ddd4edf15d6ff659e721b148656f *doc/vignette.pdf
5c6622b5d96a455a9de472480ff8f168 *extdata/AVASet/Amplicons/ProjectDef/ampliconsProject.txt
f9e763906eef2f97919ac4f794322086 *extdata/AVASet/Amplicons/Results/Align/I116/I36/I116_vs_I36.ampIds.txt
e17e6bd63e2970264d1904079f066427 *extdata/AVASet/Amplicons/Results/Align/I116/I37/I116_vs_I37.ampIds.txt
80b78bdf2a7f8f1139cac00268bf2ff5 *extdata/AVASet/Amplicons/Results/Align/I116/I40/I116_vs_I40.ampIds.txt
1aeb51619e6ca7afc923f64d9f7302e1 *extdata/AVASet/Amplicons/Results/Align/I116/I42/I116_vs_I42.ampIds.txt
1eafca9e2c3a638683c0460d0382a9f8 *extdata/AVASet/Amplicons/Results/Align/I117/I36/I117_vs_I36.ampIds.txt
bf210413caaf7a9419df8e2963975af4 *extdata/AVASet/Amplicons/Results/Align/I117/I37/I117_vs_I37.ampIds.txt
c23bc42f30b688cf4ba5caa2a5ac06f6 *extdata/AVASet/Amplicons/Results/Align/I117/I40/I117_vs_I40.ampIds.txt
6e308d49ab1298c7f1c7eac4b999a61f *extdata/AVASet/Amplicons/Results/Align/I117/I42/I117_vs_I42.ampIds.txt
8688819ae31f6f0081e4d9b505e9122d *extdata/AVASet/Amplicons/Results/Align/I118/I36/I118_vs_I36.ampIds.txt
00da7e73f4fd74e2cf72b09267283b1d *extdata/AVASet/Amplicons/Results/Align/I118/I37/I118_vs_I37.ampIds.txt
ac1a0ef2495e93115911a4eceefb5339 *extdata/AVASet/Amplicons/Results/Align/I118/I40/I118_vs_I40.ampIds.txt
fc082710ac738d02f2d202197e0499ed *extdata/AVASet/Amplicons/Results/Align/I118/I42/I118_vs_I42.ampIds.txt
351eabbfb18cd2cc7eed3a9e3f21f11d *extdata/AVASet/Amplicons/Results/Align/I9644/I36/I9644_vs_I36.ampIds.txt
121d24b7c70335c00b7ed220637e2dc2 *extdata/AVASet/Amplicons/Results/Align/I9644/I37/I9644_vs_I37.ampIds.txt
ef2122319402aad8d30da1b0552dab2c *extdata/AVASet/Amplicons/Results/Align/I9644/I40/I9644_vs_I40.ampIds.txt
77e13c09bf4125adb27b954b77c203c9 *extdata/AVASet/Amplicons/Results/Align/I9644/I42/I9644_vs_I42.ampIds.txt
cdcd883c347cd777080a19d4aa2c65d3 *extdata/AVASet/Amplicons/Results/Align/I9645/I36/I9645_vs_I36.ampIds.txt
2d620873a8819a46d8d545885033cddd *extdata/AVASet/Amplicons/Results/Align/I9645/I37/I9645_vs_I37.ampIds.txt
e8a6d900b91976e7926ca2e50c4cd60b *extdata/AVASet/Amplicons/Results/Align/I9645/I40/I9645_vs_I40.ampIds.txt
633bb52498f8d4b5b90656850bbd1e5d *extdata/AVASet/Amplicons/Results/Align/I9645/I42/I9645_vs_I42.ampIds.txt
f676b6dff2111fd80a0aed08ed179b1a *extdata/AVASet/Amplicons/Results/Align/I9646/I36/I9646_vs_I36.ampIds.txt
d9db7e5f7743f8ea294f3e01c7dbee34 *extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.ampIds.txt
907a02f83e1b3b57cecace640421043d *extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.readAlign.txt
20be25a1f9a3aaf7cd44e3a0c62f6690 *extdata/AVASet/Amplicons/Results/Align/I9646/I40/I9646_vs_I40.ampIds.txt
f1421bfaa9dd20742f761ed17bdb4249 *extdata/AVASet/Amplicons/Results/Align/I9646/I42/I9646_vs_I42.ampIds.txt
25732bf3ccfdcd0cd4e3af14e9814102 *extdata/AVASet/Amplicons/Results/Variants/I116/I116xI36detectedVariants.txt
8ea131293a25d17e6ccc43557279c3e7 *extdata/AVASet/Amplicons/Results/Variants/I116/I116xI37detectedVariants.txt
2a35c4b7dcfafae61ed38a475fae9855 *extdata/AVASet/Amplicons/Results/Variants/I116/I116xI40detectedVariants.txt
0da940096b6714b0e05c758e791215e7 *extdata/AVASet/Amplicons/Results/Variants/I116/I116xI42detectedVariants.txt
cffdd0027674433cdfb445377fabcf44 *extdata/AVASet/Amplicons/Results/Variants/I117/I117xI36detectedVariants.txt
4054216fe8bbe0d9b216ab863f28fcab *extdata/AVASet/Amplicons/Results/Variants/I117/I117xI37detectedVariants.txt
51ba32c77458a0923ba72f4a1ae37f2d *extdata/AVASet/Amplicons/Results/Variants/I117/I117xI40detectedVariants.txt
c0c28362fd5ba01a67b7a522ba3d4b16 *extdata/AVASet/Amplicons/Results/Variants/I117/I117xI42detectedVariants.txt
befc098b7639568e29db0bc4e4fd0604 *extdata/AVASet/Amplicons/Results/Variants/I118/I118xI36detectedVariants.txt
c226e75fa97609530a48c0d3746d9026 *extdata/AVASet/Amplicons/Results/Variants/I118/I118xI37detectedVariants.txt
e098d40aa1531ec98f227fcbd0d812b4 *extdata/AVASet/Amplicons/Results/Variants/I118/I118xI40detectedVariants.txt
c7ba99a72c8a05eb3b36180227930ad5 *extdata/AVASet/Amplicons/Results/Variants/I118/I118xI42detectedVariants.txt
9c8d77d0ce629224e01a98b6d416124f *extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI36detectedVariants.txt
b8901eb7b1a09d9762acb8b90b8a53b8 *extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI37detectedVariants.txt
36ed3ebe9c0fd92c90ef7c533fa2ee40 *extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI40detectedVariants.txt
34925a3123b8ed285551baa5f5c3b05d *extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI42detectedVariants.txt
20ab4c33306e69dac0271644807bdd5e *extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI36detectedVariants.txt
2e04015f25b47c251b5a61ae6d9a33fb *extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI37detectedVariants.txt
a9a627d3ce6061d0f156f6c08981e858 *extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI40detectedVariants.txt
875cbb84c2447d4310cd00bf4ce6ba01 *extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI42detectedVariants.txt
e4faca18d0584a695042df52fb484c19 *extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI36detectedVariants.txt
3d30342898e09cf1953ab2a0bab611e3 *extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI37detectedVariants.txt
3358f6f755f371172009592d08b23673 *extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI40detectedVariants.txt
356d22e54ecfe7315a7b990230a0263f *extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI42detectedVariants.txt
0a0f0e703a2c32804aba1910bb7abb55 *extdata/AVASet/Amplicons/Results/Variants/currentVariantDefs.txt
7d15f349a83b32d6c88c8867d7de3e86 *extdata/AVASet_doAmplicon/amp.csv
e6d26ae35b9fb30a4bdf645969335def *extdata/AVASet_doAmplicon/reference.csv
6e533ec95276db04d8d16672a03698a6 *extdata/AVASet_doAmplicon/sample.csv
b8376c2b5e4571c00bdcedc6d2044054 *extdata/AVASet_doAmplicon/variant.csv
457b889cadc492912613fe510b16c882 *extdata/AVASet_doAmplicon/variantHits.csv
a1523ebbbcd6680084ab2af418d53aac *extdata/AVAVarFreqExport/AVAVarFreqExport.xls
d6cb5df93e041924c899cffb4e351365 *extdata/MapperSet/N01/mapping/454HCDiffs.txt
cfd721cf0fbc0361b965f03431033a2e *extdata/MapperSet/N01/mapping/454NewblerMetrics.txt
0123840f6fa81284ee9ba76dc3b816be *extdata/MapperSet/N03/mapping/454HCDiffs.txt
fa1314c513425034298adbd2d14e3863 *extdata/MapperSet/N03/mapping/454NewblerMetrics.txt
6e01c28e047cebcabfe5c3679c765457 *extdata/MapperSet/N04/mapping/454HCDiffs.txt
b2ef968458efdbad265e962b05ff7f4f *extdata/MapperSet/N04/mapping/454NewblerMetrics.txt
e1933ee319d3fb952131e4940e509758 *extdata/SFF/example.sff
57c47448cef42618fd8bada3ec259e0c *extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.fna
b1de8bbbf428f9c68971ef61f6a125f4 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.qual
73efee4b14e5652a6ab83269b9b9ab54 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.fna
c43878f368ceeb997c9026c64fbc3f01 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.qual
d8b9dfccef6810a6c931a8e84287fee7 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.fna
a456eb560a86f0eb1180a13ba6ca0e38 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.qual
df3ac6f6d393cc83de549f7ddb465dca *extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.fna
5be49aabadf4c811b7a1f1f502b5ea20 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.qual
8db43e0e4451f5a39155ca7311e432b1 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.csv
b5c28104125e75af2e4d1acdd782bba8 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.txt
2598452339aeb58c15441ee7e0514349 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454DataProcessingDir.xml
1307d40d722c219eac816b4e118d9ac8 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.csv
a3cc5f510eeb00cadb78a300c4c5126c *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.txt
177d2fe0b330aee89997d3baf1183963 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.csv
715ed7fa09c86baa8e12515139d252a5 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.txt
4cbd0943f5c0c5e58fa223c3e0d534ae *extdata/SVDetection/R_2009_07_30/D_2009_07_31/dataRunParams.xml
b10b1b2170b7d951d06ffdcc4d7bc2a9 *extdata/SVDetection/R_2009_07_30/D_2009_07_31/gsRunProcessor.log
aefe78f4da7adb1a866c9ebc911ae92c *extdata/SVDetection/bam/N01.bam
2e8c15949f5d8bfb778d4eaa5ab56c1c *extdata/SVDetection/chip/CaptureArray_hg19.bed
5c757aea2e94fea509af660e4a4b2039 *extdata/qualityReport.Rnw
825ef80e715b485c0ff4d92810ddaf29 *help/AVASet,character,character,missing,missing,missing,missing,missing-method.html
825ef80e715b485c0ff4d92810ddaf29 *help/AVASet,character,missing,character,character,character,character,character-method.html
825ef80e715b485c0ff4d92810ddaf29 *help/AVASet,character,missing,character,character,character,missing,missing-method.html
825ef80e715b485c0ff4d92810ddaf29 *help/AVASet,character,missing,missing,missing,missing,missing,missing-method.html
722c5d1ed9f1780a7141c9cc8c261243 *help/AVASet-class.html
825ef80e715b485c0ff4d92810ddaf29 *help/AVASet.html
d73a69819e9ff31a8afb5d73765220a2 *help/AnIndex
abafd9d2419fe4b0c09b48f687fae09c *help/AnnotatedVariants-class.html
985cadcaf480bb7e58caa1547716663f *help/Breakpoints-class.html
934822d68a8c892189a063aca7ac1462 *help/MapperSet,character-method.html
7edf5d61e5572769b854c6bcac4d20a3 *help/MapperSet-class.html
934822d68a8c892189a063aca7ac1462 *help/MapperSet.html
217ca0189eee79069808569753dc334a *help/R453Plus1Toolbox.rdb
fd4f5e5f2cc3f30303a69bc8d512e3af *help/R453Plus1Toolbox.rdx
cefff74bee43a0aa51dfc20623bc6140 *help/SFFContainer-class.html
cefff74bee43a0aa51dfc20623bc6140 *help/SFFContainer.html
fc09ee542fe938504d52128fe82ec00f *help/SFFRead-class.html
fc09ee542fe938504d52128fe82ec00f *help/SFFRead.html
722c5d1ed9f1780a7141c9cc8c261243 *help/[,AVASet,ANY,ANY,ANY-method.html
722c5d1ed9f1780a7141c9cc8c261243 *help/[,AVASet,ANY,ANY-method.html
985cadcaf480bb7e58caa1547716663f *help/[,Breakpoints,ANY,ANY,ANY-method.html
985cadcaf480bb7e58caa1547716663f *help/[,Breakpoints,ANY,ANY-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/[,SFFContainer,ANY,ANY,ANY-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/[,SFFContainer,ANY,ANY-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/addRead,SFFContainer,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/addRead.html
2cfe61fc9b717ff7a2a374fdfcec397a *help/aliases.rds
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,AVASet,BSgenome,character,logical-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,AVASet,BSgenome,character,missing-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,AVASet,BSgenome,missing,logical-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,AVASet,BSgenome,missing,missing-method.html
722c5d1ed9f1780a7141c9cc8c261243 *help/alignShortReads,AVASet,DNAStringSet,character-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,DNAStringSet,BSgenome,character,logical-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,DNAStringSet,BSgenome,character,missing-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,DNAStringSet,BSgenome,missing,logical-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads,DNAStringSet,BSgenome,missing,missing-method.html
a57a8b2a379022acb0b31c49e367fc25 *help/alignShortReads.html
985cadcaf480bb7e58caa1547716663f *help/alignedReadsC1,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/alignedReadsC1.html
985cadcaf480bb7e58caa1547716663f *help/alignedReadsC2,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/alignedReadsC2.html
04c0e573441dc02b21330072d792ac33 *help/annotateVariants,AVASet,missing-method.html
722c5d1ed9f1780a7141c9cc8c261243 *help/annotateVariants,AVASet-method.html
04c0e573441dc02b21330072d792ac33 *help/annotateVariants,MapperSet,BSgenome-method.html
04c0e573441dc02b21330072d792ac33 *help/annotateVariants,MapperSet,missing-method.html
7edf5d61e5572769b854c6bcac4d20a3 *help/annotateVariants,MapperSet-method.html
04c0e573441dc02b21330072d792ac33 *help/annotateVariants,data.frame,missing-method.html
04c0e573441dc02b21330072d792ac33 *help/annotateVariants.html
abafd9d2419fe4b0c09b48f687fae09c *help/annotatedVariants,AnnotatedVariants-method.html
abafd9d2419fe4b0c09b48f687fae09c *help/annotatedVariants.html
722c5d1ed9f1780a7141c9cc8c261243 *help/assayDataAmp,AVASet-method.html
25173e822361abf538cdbc49a28df02d *help/assayDataAmp.html
3fb9b38278ee2660816c0fc7caf9da1b *help/ava2vcf,AVASet-method.html
3fb9b38278ee2660816c0fc7caf9da1b *help/ava2vcf.html
67686627235266349d14b3ea3d1a16b4 *help/avaSetExample.html
1f9a0e4b4f6f40e084a3ebcd91489907 *help/avaSetFiltered.html
ae58102a3c997a08ffc97a1ec75ad196 *help/avaSetFiltered_annot.html
1b3a0a1a984700aa233ce8ad7aaa4f29 *help/baseFrequency,DNAStringSet-method.html
1b3a0a1a984700aa233ce8ad7aaa4f29 *help/baseFrequency,SFFContainer-method.html
1b3a0a1a984700aa233ce8ad7aaa4f29 *help/baseFrequency,ShortRead-method.html
1b3a0a1a984700aa233ce8ad7aaa4f29 *help/baseFrequency.html
f5038b06d5905fcfbe0abe0f6212fdce *help/baseQualityHist,QualityScaledDNAStringSet-method.html
f5038b06d5905fcfbe0abe0f6212fdce *help/baseQualityHist,SFFContainer-method.html
f5038b06d5905fcfbe0abe0f6212fdce *help/baseQualityHist,ShortReadQ-method.html
f5038b06d5905fcfbe0abe0f6212fdce *help/baseQualityHist.html
5b98fcf528717b57a447f9a1dee8feed *help/baseQualityStats,QualityScaledDNAStringSet-method.html
5b98fcf528717b57a447f9a1dee8feed *help/baseQualityStats,SFFContainer-method.html
5b98fcf528717b57a447f9a1dee8feed *help/baseQualityStats,ShortReadQ-method.html
5b98fcf528717b57a447f9a1dee8feed *help/baseQualityStats.html
2b08b96d46017c3f85ff6987d92f0db3 *help/breakpoints.html
f0723ea9f0cb3db0cbc61f25955dbaef *help/calculateTiTv,AVASet-method.html
f0723ea9f0cb3db0cbc61f25955dbaef *help/calculateTiTv,MapperSet-method.html
f0723ea9f0cb3db0cbc61f25955dbaef *help/calculateTiTv.html
d3fa9c51d8115ba7f05514a1f4f5a472 *help/captureArray.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipAdapterLeft,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/clipAdapterLeft,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipAdapterLeft.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipAdapterRight,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/clipAdapterRight,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipAdapterRight.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipQualityLeft,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/clipQualityLeft,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipQualityLeft.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipQualityRight,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/clipQualityRight,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/clipQualityRight.html
985cadcaf480bb7e58caa1547716663f *help/commonAlignC1,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/commonAlignC1.html
985cadcaf480bb7e58caa1547716663f *help/commonAlignC2,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/commonAlignC2.html
985cadcaf480bb7e58caa1547716663f *help/commonBpsC1,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/commonBpsC1.html
985cadcaf480bb7e58caa1547716663f *help/commonBpsC2,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/commonBpsC2.html
334054e6e446b0c9e30e9d8e6b4dceac *help/complexity.dust,DNAStringSet-method.html
334054e6e446b0c9e30e9d8e6b4dceac *help/complexity.dust,SFFContainer-method.html
334054e6e446b0c9e30e9d8e6b4dceac *help/complexity.dust,ShortRead-method.html
334054e6e446b0c9e30e9d8e6b4dceac *help/complexity.dust.html
695938d7eeaf88db06e0e558286340a5 *help/complexity.entropy,DNAStringSet-method.html
695938d7eeaf88db06e0e558286340a5 *help/complexity.entropy,SFFContainer-method.html
695938d7eeaf88db06e0e558286340a5 *help/complexity.entropy,ShortRead-method.html
695938d7eeaf88db06e0e558286340a5 *help/complexity.entropy.html
0f4e02d4b43e6bde727fa46ffa9cebf4 *help/convertCigar.html
a55b9a9dea7b1d7e608bdfe97a073ac1 *help/coverageOnTarget,list,GRanges-method.html
a55b9a9dea7b1d7e608bdfe97a073ac1 *help/coverageOnTarget.html
4a28f199c9417447343875777e3a5fa6 *help/demultiplexReads,XStringSet,XStringSet,missing,logical-method.html
4a28f199c9417447343875777e3a5fa6 *help/demultiplexReads,XStringSet,XStringSet,missing,missing-method.html
4a28f199c9417447343875777e3a5fa6 *help/demultiplexReads,XStringSet,XStringSet,numeric,logical-method.html
4a28f199c9417447343875777e3a5fa6 *help/demultiplexReads,XStringSet,XStringSet,numeric,missing-method.html
4a28f199c9417447343875777e3a5fa6 *help/demultiplexReads.html
60e2b9aae9a5b9ea69b7248e2a7b5cc9 *help/detectBreakpoints,list-method.html
60e2b9aae9a5b9ea69b7248e2a7b5cc9 *help/detectBreakpoints.html
0d17515c8fb3c865c7e9383049a0c809 *help/dinucleotideOddsRatio,DNAStringSet-method.html
0d17515c8fb3c865c7e9383049a0c809 *help/dinucleotideOddsRatio,SFFContainer-method.html
0d17515c8fb3c865c7e9383049a0c809 *help/dinucleotideOddsRatio,ShortRead-method.html
0d17515c8fb3c865c7e9383049a0c809 *help/dinucleotideOddsRatio.html
0f4e02d4b43e6bde727fa46ffa9cebf4 *help/extendedCIGARToList.html
722c5d1ed9f1780a7141c9cc8c261243 *help/fDataAmp,AVASet-method.html
34abf381a9a5bbade1ee06e967db5148 *help/fDataAmp.html
722c5d1ed9f1780a7141c9cc8c261243 *help/featureDataAmp,AVASet-method.html
cf09e97be0c139ba0694e46d4a43c687 *help/featureDataAmp.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,IntegerRangesList,DNAString,missing,missing-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,IntegerRangesList,DNAString,numeric,numeric-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,IntegerRangesList,missing,missing,missing-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,IntegerRangesList,missing,numeric,numeric-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,missing,DNAString,missing,missing-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,missing,DNAString,numeric,numeric-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,missing,missing,missing,missing-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads,list,missing,missing,numeric,numeric-method.html
9a8a201ac3bab8f5e41154751ead7b1e *help/filterChimericReads.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowChars,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/flowChars,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowChars.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowIndexes,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/flowIndexes,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowIndexes.html
fc09ee542fe938504d52128fe82ec00f *help/flowgram,SFFRead-method.html
fc09ee542fe938504d52128fe82ec00f *help/flowgram.html
1424a7c5137621498b496d6b5b75ffdd *help/flowgramBarplot,SFFRead-method.html
1424a7c5137621498b496d6b5b75ffdd *help/flowgramBarplot.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowgramFormat,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/flowgramFormat,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowgramFormat.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowgrams,SFFContainer-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/flowgrams.html
119d7cf072ad7ed988db72686cd5b58a *help/gcContent,DNAStringSet-method.html
119d7cf072ad7ed988db72686cd5b58a *help/gcContent,SFFContainer-method.html
119d7cf072ad7ed988db72686cd5b58a *help/gcContent,ShortRead-method.html
119d7cf072ad7ed988db72686cd5b58a *help/gcContent.html
760f35671c1349468e1ff21a79ad7876 *help/gcContentHist,DNAStringSet-method.html
760f35671c1349468e1ff21a79ad7876 *help/gcContentHist,SFFContainer-method.html
760f35671c1349468e1ff21a79ad7876 *help/gcContentHist,ShortRead-method.html
760f35671c1349468e1ff21a79ad7876 *help/gcContentHist.html
454a12989d468003c9641592cfb14ac0 *help/gcPerPosition,DNAStringSet-method.html
454a12989d468003c9641592cfb14ac0 *help/gcPerPosition,SFFContainer-method.html
454a12989d468003c9641592cfb14ac0 *help/gcPerPosition,ShortRead-method.html
454a12989d468003c9641592cfb14ac0 *help/gcPerPosition.html
fc5601fbffc54fc220d1952dced687e3 *help/genomeSequencerMIDs,character-method.html
fc5601fbffc54fc220d1952dced687e3 *help/genomeSequencerMIDs,missing-method.html
fc5601fbffc54fc220d1952dced687e3 *help/genomeSequencerMIDs.html
97dd9a699e11dbce0f76d75b0d0aab5b *help/getAlignedReads,AVASet-method.html
97dd9a699e11dbce0f76d75b0d0aab5b *help/getAlignedReads.html
6c441693fb603f764b1a7de8c05cae70 *help/getAminoAbbr.html
cefff74bee43a0aa51dfc20623bc6140 *help/getRead,SFFContainer,character-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/getRead.html
7edf5d61e5572769b854c6bcac4d20a3 *help/getReadStatus,MapperSet-method.html
7edf5d61e5572769b854c6bcac4d20a3 *help/getReadStatus.html
722c5d1ed9f1780a7141c9cc8c261243 *help/getVariantPercentages,AVASet-method.html
7edf5d61e5572769b854c6bcac4d20a3 *help/getVariantPercentages,MapperSet-method.html
904b8de414b175b4e58a0419a7b8e380 *help/getVariantPercentages.html
072aa05ae075371d444ff079e62c6055 *help/homopolymerHist,SFFRead-method.html
072aa05ae075371d444ff079e62c6055 *help/homopolymerHist.html
722c5d1ed9f1780a7141c9cc8c261243 *help/htmlReport,AVASet-method.html
7edf5d61e5572769b854c6bcac4d20a3 *help/htmlReport,MapperSet-method.html
adf3a20ef5909de3e9ec27d55e1599d8 *help/htmlReport.html
cefff74bee43a0aa51dfc20623bc6140 *help/keySequence,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/keySequence,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/keySequence.html
985cadcaf480bb7e58caa1547716663f *help/length,Breakpoints-method.html
0f4e02d4b43e6bde727fa46ffa9cebf4 *help/listToExtendedCIGAR.html
2552cedf9d65f3db43f6e10c027658fb *help/mapperSetExample.html
985cadcaf480bb7e58caa1547716663f *help/mergeBreakpoints,Breakpoints,missing,list-method.html
985cadcaf480bb7e58caa1547716663f *help/mergeBreakpoints,Breakpoints,missing,missing-method.html
985cadcaf480bb7e58caa1547716663f *help/mergeBreakpoints,Breakpoints,numeric,missing-method.html
59a0910bd545276801c23d3457466460 *help/mergeBreakpoints.html
d2d1cf0626d4caf7f0c06ee247c046ff *help/mutationInfo.html
cefff74bee43a0aa51dfc20623bc6140 *help/name,SFFContainer-method.html
fc09ee542fe938504d52128fe82ec00f *help/name,SFFRead-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/name.html
abafd9d2419fe4b0c09b48f687fae09c *help/names,AnnotatedVariants-method.html
985cadcaf480bb7e58caa1547716663f *help/names,Breakpoints-method.html
d0d69ad28cfe2262e3d5f9c37994e82c *help/nucleotideCharts,DNAStringSet-method.html
d0d69ad28cfe2262e3d5f9c37994e82c *help/nucleotideCharts,SFFContainer-method.html
d0d69ad28cfe2262e3d5f9c37994e82c *help/nucleotideCharts,ShortRead-method.html
d0d69ad28cfe2262e3d5f9c37994e82c *help/nucleotideCharts.html
875365e67da501376c1a523a9d97e57b *help/paths.rds
a8647f15f08754811608740ad0bc98fe *help/plotAmpliconCoverage,AVASet,character,logical-method.html
a8647f15f08754811608740ad0bc98fe *help/plotAmpliconCoverage,AVASet,character,missing-method.html
a8647f15f08754811608740ad0bc98fe *help/plotAmpliconCoverage,AVASet,missing,logical-method.html
a8647f15f08754811608740ad0bc98fe *help/plotAmpliconCoverage,AVASet,missing,missing-method.html
a8647f15f08754811608740ad0bc98fe *help/plotAmpliconCoverage.html
985cadcaf480bb7e58caa1547716663f *help/plotChimericReads,Breakpoints-method.html
90b4826096007fe01bd8c8a2fd8a49aa *help/plotChimericReads.html
43cf44845bfd0d82eb54ce1e4831ccac *help/plotVariants,AnnotatedVariants,character-method.html
43cf44845bfd0d82eb54ce1e4831ccac *help/plotVariants,data.frame,character-method.html
43cf44845bfd0d82eb54ce1e4831ccac *help/plotVariants.html
f07aae8ea1a695027bd28c038664c836 *help/plotVariationFrequency,character,numeric-method.html
f07aae8ea1a695027bd28c038664c836 *help/plotVariationFrequency.html
742e41506f2808888a264035f192d8b2 *help/positionQualityBoxplot,QualityScaledDNAStringSet-method.html
742e41506f2808888a264035f192d8b2 *help/positionQualityBoxplot,SFFContainer-method.html
742e41506f2808888a264035f192d8b2 *help/positionQualityBoxplot,ShortReadQ-method.html
742e41506f2808888a264035f192d8b2 *help/positionQualityBoxplot.html
fc09ee542fe938504d52128fe82ec00f *help/quality,SFFRead-method.html
1493b1fdb2b5efeb3c754c3ea5a3d3d5 *help/qualityReportSFF.html
fc09ee542fe938504d52128fe82ec00f *help/read,SFFRead-method.html
fc09ee542fe938504d52128fe82ec00f *help/read.html
5ad282bd01c341f62d7cd9d315cc9f03 *help/readLengthHist,DNAStringSet-method.html
5ad282bd01c341f62d7cd9d315cc9f03 *help/readLengthHist,SFFContainer-method.html
5ad282bd01c341f62d7cd9d315cc9f03 *help/readLengthHist,ShortRead-method.html
5ad282bd01c341f62d7cd9d315cc9f03 *help/readLengthHist.html
dcd08d8725357c5d971801257396ea82 *help/readLengthStats,DNAStringSet-method.html
dcd08d8725357c5d971801257396ea82 *help/readLengthStats,SFFContainer-method.html
dcd08d8725357c5d971801257396ea82 *help/readLengthStats,ShortRead-method.html
dcd08d8725357c5d971801257396ea82 *help/readLengthStats.html
2b2979b6d6de8d7d2ec5a29b0d29ef53 *help/readSFF.html
cefff74bee43a0aa51dfc20623bc6140 *help/reads,SFFContainer-method.html
cefff74bee43a0aa51dfc20623bc6140 *help/reads.html
22e809d97e397318a3b307e8e7a94d14 *help/readsOnTarget,list,GRanges-method.html
22e809d97e397318a3b307e8e7a94d14 *help/readsOnTarget.html
722c5d1ed9f1780a7141c9cc8c261243 *help/referenceSequences,AVASet-method.html
18722a7999a738b17ffcc166c6a4afae *help/referenceSequences.html
fe0fed4aaaf2396eba0c1e8b4f17d12d *help/regions.html
ece98a85878a99fe1ca74bbdfe0e58e7 *help/removeLinker,XStringSet,DNAString,logical,numeric,numeric-method.html
ece98a85878a99fe1ca74bbdfe0e58e7 *help/removeLinker,XStringSet,DNAString,missing,missing,missing-method.html
ece98a85878a99fe1ca74bbdfe0e58e7 *help/removeLinker.html
985cadcaf480bb7e58caa1547716663f *help/seqsC1,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/seqsC1.html
985cadcaf480bb7e58caa1547716663f *help/seqsC2,Breakpoints-method.html
985cadcaf480bb7e58caa1547716663f *help/seqsC2.html
2d6d8b1313ca39d1f61ddb7507428fbd *help/sequenceCaptureLinkers,character-method.html
2d6d8b1313ca39d1f61ddb7507428fbd *help/sequenceCaptureLinkers,missing-method.html
2d6d8b1313ca39d1f61ddb7507428fbd *help/sequenceCaptureLinkers.html
4407082819a42fd50b4346f2dc1efa9f *help/sequenceQualityHist,QualityScaledDNAStringSet-method.html
4407082819a42fd50b4346f2dc1efa9f *help/sequenceQualityHist,SFFContainer-method.html
4407082819a42fd50b4346f2dc1efa9f *help/sequenceQualityHist,ShortReadQ-method.html
4407082819a42fd50b4346f2dc1efa9f *help/sequenceQualityHist.html
722c5d1ed9f1780a7141c9cc8c261243 *help/setVariantFilter,AVASet-method.html
7edf5d61e5572769b854c6bcac4d20a3 *help/setVariantFilter,MapperSet-method.html
19a52b6904c518cc0ee6c051d172eddb *help/setVariantFilter.html
d1b2cc2a15d76c1b3021ec11ce2212ee *help/sff2fastq,SFFContainer-method.html
d1b2cc2a15d76c1b3021ec11ce2212ee *help/sff2fastq.html
3a8af15c72f0c7397cb7fac4c1f59a9f *help/variants.html
dd0d62984587b99b4cf340b750ecb17d *help/writeSFF.html
8a9ff7ffc744e360dfe29ed656c683ba *html/00Index.html
2e284d8096e8f8462627cf411fbfbc09 *html/AVASet-class.html
bd064871601cd7c3ba80bb6f002e6f17 *html/AVASet.html
64d57527245f424190737949a090e3ab *html/AnnotatedVariants-class.html
5c8dc70baf2de547dcd77b9cd193785b *html/Breakpoints-class.html
021d08c073d3a2802876169ce0ee8363 *html/MapperSet-class.html
095494eccfb0ab5a982f9c34b5c59c73 *html/MapperSet.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
c86ea461414936d09243671717f6e07e *html/SFFContainer-class.html
82ff83c7bc330d096a8cf1272d3a15bb *html/SFFRead-class.html
6120de6d484cd62a162548c3fe76f4f3 *html/alignShortReads.html
a2820c65b150ed4b5c4e82880e0f41ec *html/annotateVariants.html
d64ea6804f29112f46517166028107b6 *html/assayDataAmp.html
750a573f916997d42a14e146cd2785ad *html/ava2vcf.html
96723014045033e9cef0d00321cf5eda *html/avaSetExample.html
7b0f196ce441cc53ea7fa493a7802948 *html/avaSetFiltered.html
d5e3dc8dd28ef909df4a71610c145134 *html/avaSetFiltered_annot.html
666e23ccfb1a83e64427072b062de870 *html/baseFrequency.html
da841b2ecae0c7bb19a8477da436c717 *html/baseQualityHist.html
7cc7c67a401f6c6e353c4fa432474485 *html/baseQualityStats.html
c5d33ff84e03590d2f99fc3335dc6851 *html/breakpoints.html
6fee1c5cfc57a84929de849456cdb2b5 *html/calculateTiTv.html
ff413edd573bb543fdff0beecdc5c559 *html/captureArray.html
28e57d3184b02ee861839589d0df087a *html/complexity.dust.html
a43c194f173c3db62a9f0ca0a157613c *html/complexity.entropy.html
e81b2538a5cad13afd8ff56a8cb89d94 *html/convertCigar.html
53e53c1b002fdff54c1a1dedbf193c34 *html/coverageOnTarget.html
e96fc83c7a4e557321299a6064159040 *html/demultiplexReads.html
ab0694b5249b59659e6480ec99217351 *html/detectBreakpoints.html
7ba7074c89cfcecd7b28640dd5971f7f *html/dinucleotideOddsRatio.html
653ee4d6c6a4e1723d837b673a3e8c01 *html/fDataAmp.html
05e341f06db2e409936797011b5b8254 *html/featureDataAmp.html
02d9f4aa740d5d20935afaa7b5c776e8 *html/filterChimericReads.html
0bd8e9d29f2b252d0ca7335a5a81a66f *html/flowgramBarplot.html
0e3f8b3f41ad8f593e4332ecd45737d0 *html/gcContent.html
b52e3f5763a90b01c1e70105c3e68993 *html/gcContentHist.html
2daed24fc90bed217ab445cb1bf9553c *html/gcPerPosition.html
d0cfc345fa14eb9af6709d1579938321 *html/genomeSequencerMIDs.html
3a3857f670b229aaff7e0ec3efb40668 *html/getAlignedReads.html
82f0dcdbc9c458eb350aa172c8d05b9d *html/getAminoAbbr.html
f6c6a6033bb67278190f5428b271d7e0 *html/getVariantPercentages.html
df496b63c92957a3ff8320cc9163fd5c *html/homopolymerHist.html
46248c00b79ff414c59454566234b865 *html/htmlReport.html
03c781c53baf2c93cb2324afa3be1ed7 *html/mapperSetExample.html
daae3d358f4fdca98742f1d62802c649 *html/mergeBreakpoints.html
1d93ce51952b787abf4e5f683f0b4d9b *html/mutationInfo.html
2774ee94d98cd69a5d1a909b248ced03 *html/nucleotideCharts.html
3cd1ae76a1fab57f37dd62147777275d *html/plotAmpliconCoverage.html
07b4ef0c80e6aeb0acf4c54f0db7d35f *html/plotChimericReads.html
126f85ccbab8031557a591d5dccba5bb *html/plotVariants.html
3fde030e4de6ae3b4487fa26e978dbc3 *html/plotVariationFrequency.html
6c53207ea29ebaab639f2bf00e872968 *html/positionQualityBoxplot.html
5ea9da849c3dcde33c077811efa1d640 *html/qualityReportSFF.html
f3a25207bf670d82f35ba60c604f2654 *html/readLengthHist.html
c51968a667f1343182a2a71d875b9a9c *html/readLengthStats.html
cbf223f4b0a9899c4b34e387ac980442 *html/readSFF.html
116bf62c7a087ea396ea630928049850 *html/readsOnTarget.html
ef3443a3fd5f05ea0ddf7ba6bdeea710 *html/referenceSequences.html
8ca735f3e5d790902ef6c67f88a88fcd *html/regions.html
4f8f44929ca8e704605e6c2b111d0408 *html/removeLinker.html
0921ae2cc69f4d90aa8ec2bfdc5a46d6 *html/sequenceCaptureLinkers.html
0cdf80b87d8b2bdacf26a038b98e9fb7 *html/sequenceQualityHist.html
191a562fae65d9d73ffdd86c1a9806b1 *html/setVariantFilter.html
cee9d915a3d9c332b16889a5ed8d837d *html/sff2fastq.html
1308aa50e2b9e95290cba6a7aa34dfc2 *html/variants.html
ac6a48f339cea65dfb35579392219b12 *html/writeSFF.html
b103eb1265a62f9f6a7ebf7519891ce7 *javascript/sorttable.js
708c8c274eb551d645edd388f40c9465 *libs/i386/R453Plus1Toolbox.dll
afebad04cb768bb9e00901eec955a7de *libs/x64/R453Plus1Toolbox.dll
