d4bf401c8ee4fbc0f84ea6ee9da7aaea *CITATION
d50e975b9a025e83a47f0d02cbc6bd7e *DESCRIPTION
3ae5dc40a54c70967ebde918dd2e4b05 *INDEX
5cc42acc99607a6910a79cce6cbaf690 *Meta/Rd.rds
980e08c3c7fbba76a50993f14c3ef74d *Meta/data.rds
8503e676975364d771072956cdbca633 *Meta/features.rds
ac0e388d280ce2597a6a5c9c2b18e31f *Meta/hsearch.rds
80d7671f5c6ee6858cf687adcd3859d9 *Meta/links.rds
3a1f89bf997b56fad122aa3a349d6c45 *Meta/nsInfo.rds
927521b4ae36e1ac4f2e3297102a48ef *Meta/package.rds
b5f0c15f94c0060bf9f49a246ef39620 *Meta/vignette.rds
d01e66deba1be86b1fea33655911d3fe *NAMESPACE
a0c18fbbc9ede6018b88781318006c7f *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/easyRNASeq
363ec055f20dff82d0cca0e4b384b32b *R/easyRNASeq.rdb
b9ebbc75f5332cac776a1e6ddc819109 *R/easyRNASeq.rdx
5d0200d7ecbedb5d9e9536babedca3f2 *data/RobinsonDelhomme2014.txt.gz
c4c89e7eb031240287f39bd66a259566 *doc/01-Introduction.Rmd
2e7d68f8948c27d87c6307f5fe155c10 *doc/02-AnnotParam.Rmd
318b6d3b2181a622c980bd45d1a0eddf *doc/03-SyntheticTranscripts.Rmd
5cccebc516f7427a569a20776797b3f5 *doc/04-BamParam.Rmd
33f077e8defd643fb9d0ebd5cfcd07d5 *doc/05-RnaSeqParam.Rmd
6c61d35ace121d29a50b06b1da084c48 *doc/06-simpleRNASeq.Rmd
048307962a774976e00d7f4258a6850f *doc/07-cleanUp.Rmd
e55a4079749339ac9b5f0d610de27c00 *doc/08-Session-Info.Rmd
d41d8cd98f00b204e9800998ecf8427e *doc/09-Acknowledgments.Rmd
958f1eafa6cbc2fb936ff923e6ee2e86 *doc/10-Foonotes.Rmd
d41d8cd98f00b204e9800998ecf8427e *doc/11-Images.Rmd
7d88cc2503a48f4ec8937c362e25440c *doc/12-Appendix.Rmd
b947f259ef07eac1004455952dd247d9 *doc/202_subset_sortmerna_trimmomatic_sorted.bam
d223e774ae3dfb6c4a61a8290dfcfb4f *doc/207_subset_sortmerna_trimmomatic_sorted.bam
958606146d6225c633a6d17e26c582af *doc/213.1_subset_sortmerna_trimmomatic_sorted.bam
d2edacac18a8dd4e00cfe63199643235 *doc/221_subset_sortmerna_trimmomatic_sorted.bam
e8e3f100a7b294aab407d5a395bd4238 *doc/226.1_subset_sortmerna_trimmomatic_sorted.bam
5497bf28a6e9b159180b9065d92abde0 *doc/229.1_subset_sortmerna_trimmomatic_sorted.bam
7f01514be0a71458becb5aef321414c8 *doc/Bibliography/References.bib
943035d7888d0ba3fee34a28adde3dfc *doc/easyRNASeq.R
ac92dbf5b6026eb5836d3acadc6db3b8 *doc/easyRNASeq.Rnw
cc85fce792de243fcdf19c207a938c8d *doc/easyRNASeq.pdf
ae1aaaa908882bb6af02f8ae64c47c54 *doc/index.html
000c6ce4a403b3c05d04dccd8e92d938 *doc/simpleRNASeq.R
289ef9ef497ee9f4b3d6c5274acbb35e *doc/simpleRNASeq.Rmd
bed6f25f8e61d7598f81220013402fc1 *doc/simpleRNASeq.html
5c82376e8d480f99d28c6fc2ff553e08 *help/ANNOTATION.TYPE.html
c6e03f0d64a543cea9d1752736244c8b *help/AnIndex
d4062a7ccd593f793484485acf895993 *help/AnnotParam+20class.html
cf9765aa6914dc540171bbadee8e8597 *help/AnnotParam+20internal+20methods.html
72138286df6c830ca7c8f4d3500c24d9 *help/AnnotParam+2CGRanges-method.html
72138286df6c830ca7c8f4d3500c24d9 *help/AnnotParam+2Ccharacter-method.html
72138286df6c830ca7c8f4d3500c24d9 *help/AnnotParam+2Cmissing-method.html
1e9d19dde28d60257f9ae26baebd5e20 *help/AnnotParam-accessors.html
d4062a7ccd593f793484485acf895993 *help/AnnotParam-class.html
bcbb864a8d26ef975c0aac3aac24c213 *help/AnnotParam.html
d4062a7ccd593f793484485acf895993 *help/AnnotParamCharacter-class.html
d4062a7ccd593f793484485acf895993 *help/AnnotParamObject-class.html
2779c661f4da8a9996eab3d8c01cd994 *help/BamFileList-class.html
2779c661f4da8a9996eab3d8c01cd994 *help/BamFileList.html
9c307766da1d91a4d3b263f3490d8fde *help/BamParam+20class.html
6a911489fe568a7470b2f202815abf69 *help/BamParam+2CANY-method.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/BamParam-accessors.html
9c307766da1d91a4d3b263f3490d8fde *help/BamParam-class.html
bcbb864a8d26ef975c0aac3aac24c213 *help/BamParam.html
46042271dfcfa084e2687ba110b7163d *help/BiocFileCache+20methods.html
46042271dfcfa084e2687ba110b7163d *help/BiocFileCache-methods.html
8dbf20b979652441c6a37d46a6b8c54d *help/Defunct+20functions.html
2779c661f4da8a9996eab3d8c01cd994 *help/GRanges-class.html
2779c661f4da8a9996eab3d8c01cd994 *help/GRanges.html
5c82376e8d480f99d28c6fc2ff553e08 *help/GTF.FIELDS.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/GenomicRanges-methods.html
a2fb3028e3257aff79e7eadbc126088a *help/IRanges+20additional+20methods.html
a2fb3028e3257aff79e7eadbc126088a *help/IRanges-methods.html
2779c661f4da8a9996eab3d8c01cd994 *help/IRanges.html
f7129d3a170b73f20b2df28b32e73829 *help/RNAseq+20class.html
f7129d3a170b73f20b2df28b32e73829 *help/RNAseq-class.html
f7129d3a170b73f20b2df28b32e73829 *help/RNAseq.html
ec7a740488067a6965b04000e786e379 *help/RPKM+2CRNAseq+2CANY+2CANY+2CANY-method.html
ec7a740488067a6965b04000e786e379 *help/RPKM+2CRNAseq-method.html
ec7a740488067a6965b04000e786e379 *help/RPKM+2Cmatrix+2CANY+2Cvector+2Cvector-method.html
ec7a740488067a6965b04000e786e379 *help/RPKM.html
2779c661f4da8a9996eab3d8c01cd994 *help/RangedSummarizedExperiment-class.html
dcd1152c7f920b9e9a195999b37bed8d *help/RnaSeqParam+20class.html
aa5c30d713a828a9c09731ded786a133 *help/RnaSeqParam+2CANY-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/RnaSeqParam-accessors.html
dcd1152c7f920b9e9a195999b37bed8d *help/RnaSeqParam-class.html
aa5c30d713a828a9c09731ded786a133 *help/RnaSeqParam.html
430e43f0abdcceec373462c64a6dc614 *help/RobinsonDelhomme2014.html
1ba36bc2a14615c93b5e613f7c7e8192 *help/Rsamtools-methods.html
2779c661f4da8a9996eab3d8c01cd994 *help/SRFilterResult.html
2d54f6b9d1fa209b666043405ee691bb *help/ShortRead+20additional+20methods.html
2d54f6b9d1fa209b666043405ee691bb *help/ShortRead-methods.html
2779c661f4da8a9996eab3d8c01cd994 *help/SummarizedExperiment.html
5c82376e8d480f99d28c6fc2ff553e08 *help/TUTORIAL.DATA.html
5c82376e8d480f99d28c6fc2ff553e08 *help/VIGNETTE.DATA.html
2761e23515509397489d6738ea8a4450 *help/accessors.html
866d72e86fd13f1c1576c1da30a04f84 *help/aliases.rds
2d54f6b9d1fa209b666043405ee691bb *help/alignData.html
bcbb864a8d26ef975c0aac3aac24c213 *help/annotParam+2CRnaSeqParam-method.html
2779c661f4da8a9996eab3d8c01cd994 *help/assay.html
bcbb864a8d26ef975c0aac3aac24c213 *help/bamParam+2CRnaSeqParam-method.html
2d54f6b9d1fa209b666043405ee691bb *help/barcodePlot+2CAlignedRead-method.html
2d54f6b9d1fa209b666043405ee691bb *help/barcodePlot+2CDNAStringSet-method.html
2d54f6b9d1fa209b666043405ee691bb *help/barcodePlot+2CShortReadQ-method.html
2d54f6b9d1fa209b666043405ee691bb *help/barcodePlot.html
945dd691a2f7971cdb0398359b12e3dd *help/basename+20methods.html
945dd691a2f7971cdb0398359b12e3dd *help/basename+2CBamFile-method.html
945dd691a2f7971cdb0398359b12e3dd *help/basename+2CBamFileList-method.html
945dd691a2f7971cdb0398359b12e3dd *help/basename-methods.html
945dd691a2f7971cdb0398359b12e3dd *help/basename.html
2d54f6b9d1fa209b666043405ee691bb *help/chastityFilter+2CSRFilter-method.html
2d54f6b9d1fa209b666043405ee691bb *help/chastityFilter.html
2761e23515509397489d6738ea8a4450 *help/chrSize+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/chrSize+3C-+2CRNAseq+2Cinteger-method.html
2761e23515509397489d6738ea8a4450 *help/chrSize+3C-+2CRNAseq+2Clist-method.html
2761e23515509397489d6738ea8a4450 *help/chrSize+3C-.html
2761e23515509397489d6738ea8a4450 *help/chrSize.html
2779c661f4da8a9996eab3d8c01cd994 *help/chromosomeFilter.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/colnames+2CGRanges-method.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/colnames+2CGRangesList-method.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/colnames.html
2779c661f4da8a9996eab3d8c01cd994 *help/compose.html
bcbb864a8d26ef975c0aac3aac24c213 *help/countBy+2CRnaSeqParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/countBy.html
3719941f5b246dcc4080fa21f17fc9c1 *help/createSyntheticTranscripts+2CAnnotParamCharacter-method.html
3719941f5b246dcc4080fa21f17fc9c1 *help/createSyntheticTranscripts+2Ccharacter-method.html
3719941f5b246dcc4080fa21f17fc9c1 *help/createSyntheticTranscripts.html
1e9d19dde28d60257f9ae26baebd5e20 *help/datasource+2CAnnotParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/datasource+2CRnaSeqParam-method.html
1e9d19dde28d60257f9ae26baebd5e20 *help/datasource.html
2d54f6b9d1fa209b666043405ee691bb *help/demultiplex+2CAlignedRead-method.html
2d54f6b9d1fa209b666043405ee691bb *help/demultiplex+2CDNAStringSet-method.html
2d54f6b9d1fa209b666043405ee691bb *help/demultiplex+2CShortReadQ-method.html
2d54f6b9d1fa209b666043405ee691bb *help/demultiplex.html
1e9d19dde28d60257f9ae26baebd5e20 *help/easyRNASeq+20AnnotParam+20accessors.html
72138286df6c830ca7c8f4d3500c24d9 *help/easyRNASeq+20AnnotParam+20constructor.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/easyRNASeq+20BamParam+20accessors.html
6a911489fe568a7470b2f202815abf69 *help/easyRNASeq+20BamParam+20constructor.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/easyRNASeq+20GenomicRanges+20package+20extension.html
bcbb864a8d26ef975c0aac3aac24c213 *help/easyRNASeq+20RnaSeqParam+20accessors.html
aa5c30d713a828a9c09731ded786a133 *help/easyRNASeq+20RnaSeqParam+20constructor.html
2761e23515509397489d6738ea8a4450 *help/easyRNASeq+20accessors.html
c8838625e0ba3f89667d24bbd5311583 *help/easyRNASeq+20annotation+20internal+20methods.html
54eaf7a19db204f5e337d4407fa80fce *help/easyRNASeq+20annotation+20methods.html
ec7a740488067a6965b04000e786e379 *help/easyRNASeq+20correction+20methods.html
22fb02cc4c19c79172db191f23c1994a *help/easyRNASeq+20coverage+20methods.html
d08a96feee0d1a89c6b8470ce0d4b657 *help/easyRNASeq+20defunct+20annotation+20methods.html
50770759dfaa7949563225279fa89f9e *help/easyRNASeq+20internal+20methods.html
5e8a9b1b83f19d20c240e22e58dbdebf *help/easyRNASeq+20island+20methods.html
2779c661f4da8a9996eab3d8c01cd994 *help/easyRNASeq+20package.html
ff3eeeb27377960619e3d6ea659609a8 *help/easyRNASeq+20summarization+20internal+20methods.html
ec6c36e239ab7d422515266846a8c2e3 *help/easyRNASeq+20summarization+20methods.html
8dbf20b979652441c6a37d46a6b8c54d *help/easyRNASeq+2CRNAseq-method.html
075298872fda39bf42d786067f1fc934 *help/easyRNASeq+2Ccharacter-method.html
1e9d19dde28d60257f9ae26baebd5e20 *help/easyRNASeq-AnnotParam-accessors.html
d4062a7ccd593f793484485acf895993 *help/easyRNASeq-AnnotParam-class.html
72138286df6c830ca7c8f4d3500c24d9 *help/easyRNASeq-AnnotParam.html
3d72a83d47676f929cbf855a1fdd2e4b *help/easyRNASeq-BamFileList.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/easyRNASeq-BamParam-accessors.html
9c307766da1d91a4d3b263f3490d8fde *help/easyRNASeq-BamParam-class.html
6a911489fe568a7470b2f202815abf69 *help/easyRNASeq-BamParam.html
bcbb864a8d26ef975c0aac3aac24c213 *help/easyRNASeq-RnaSeqParam-accessors.html
dcd1152c7f920b9e9a195999b37bed8d *help/easyRNASeq-RnaSeqParam-class.html
aa5c30d713a828a9c09731ded786a133 *help/easyRNASeq-RnaSeqParam.html
2761e23515509397489d6738ea8a4450 *help/easyRNASeq-accessors.html
c8838625e0ba3f89667d24bbd5311583 *help/easyRNASeq-annotation-internal-methods.html
54eaf7a19db204f5e337d4407fa80fce *help/easyRNASeq-annotation-methods.html
f7129d3a170b73f20b2df28b32e73829 *help/easyRNASeq-class.html
ec7a740488067a6965b04000e786e379 *help/easyRNASeq-correction-methods.html
22fb02cc4c19c79172db191f23c1994a *help/easyRNASeq-coverage-methods.html
430e43f0abdcceec373462c64a6dc614 *help/easyRNASeq-datasets.html
d08a96feee0d1a89c6b8470ce0d4b657 *help/easyRNASeq-defunct-annotation-methods.html
075298872fda39bf42d786067f1fc934 *help/easyRNASeq-defunct.html
075298872fda39bf42d786067f1fc934 *help/easyRNASeq-easyRNASeq.html
5c82376e8d480f99d28c6fc2ff553e08 *help/easyRNASeq-global-variables.html
cf9765aa6914dc540171bbadee8e8597 *help/easyRNASeq-internal-AnnotParam-methods.html
50770759dfaa7949563225279fa89f9e *help/easyRNASeq-internal-methods.html
5e8a9b1b83f19d20c240e22e58dbdebf *help/easyRNASeq-island-methods.html
2779c661f4da8a9996eab3d8c01cd994 *help/easyRNASeq-package.html
a0f90f3a520473f86883d6238462b9bb *help/easyRNASeq-simpleRNASeq.html
ff3eeeb27377960619e3d6ea659609a8 *help/easyRNASeq-summarization-internal-methods.html
ec6c36e239ab7d422515266846a8c2e3 *help/easyRNASeq-summarization-methods.html
3719941f5b246dcc4080fa21f17fc9c1 *help/easyRNASeq-synthetic-transcripts.html
8dbf20b979652441c6a37d46a6b8c54d *help/easyRNASeq.html
e54824393836468171fc814416d042e7 *help/easyRNASeq.rdb
733f69c43a448ff9ebd0f6d0d317e2b7 *help/easyRNASeq.rdx
6732a96df64feada11b0a79991a2816b *help/edgeR+20additional+20methods.html
6732a96df64feada11b0a79991a2816b *help/edgeR-methods.html
ec6c36e239ab7d422515266846a8c2e3 *help/exonCounts+2CRNAseq-method.html
ec6c36e239ab7d422515266846a8c2e3 *help/exonCounts.html
ec6c36e239ab7d422515266846a8c2e3 *help/featureCounts+2CRNAseq-method.html
ec6c36e239ab7d422515266846a8c2e3 *help/featureCounts.html
d08a96feee0d1a89c6b8470ce0d4b657 *help/fetchAnnotation-defunct.html
8dbf20b979652441c6a37d46a6b8c54d *help/fetchAnnotation.html
8dbf20b979652441c6a37d46a6b8c54d *help/fetchCoverage+2CRNAseq-method.html
22fb02cc4c19c79172db191f23c1994a *help/fetchCoverage-deprecated.html
8dbf20b979652441c6a37d46a6b8c54d *help/fetchCoverage.html
46042271dfcfa084e2687ba110b7163d *help/fetchData+2Ccharacter-method.html
46042271dfcfa084e2687ba110b7163d *help/fetchData.html
21a913cc8bffd477a7a10d5f25550ee1 *help/file.exists+20methods.html
21a913cc8bffd477a7a10d5f25550ee1 *help/file.exists+2CBamFile-method.html
21a913cc8bffd477a7a10d5f25550ee1 *help/file.exists-methods.html
21a913cc8bffd477a7a10d5f25550ee1 *help/file.exists.html
2761e23515509397489d6738ea8a4450 *help/fileName+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/fileName+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/fileName+3C-.html
2761e23515509397489d6738ea8a4450 *help/fileName.html
5e8a9b1b83f19d20c240e22e58dbdebf *help/findIslands+2CRNAseq-method.html
5e8a9b1b83f19d20c240e22e58dbdebf *help/findIslands.html
ec6c36e239ab7d422515266846a8c2e3 *help/geneCounts+2CRNAseq-method.html
ec6c36e239ab7d422515266846a8c2e3 *help/geneCounts.html
2761e23515509397489d6738ea8a4450 *help/geneModel+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/geneModel+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/geneModel+3C-.html
2761e23515509397489d6738ea8a4450 *help/geneModel.html
9abe592b9f3ebffef876240ce40ea3e6 *help/genomeIntervals+20additional+20methods.html
9abe592b9f3ebffef876240ce40ea3e6 *help/genomeIntervals-methods.html
2761e23515509397489d6738ea8a4450 *help/genomicAnnotation+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/genomicAnnotation+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/genomicAnnotation+3C-.html
2761e23515509397489d6738ea8a4450 *help/genomicAnnotation.html
54eaf7a19db204f5e337d4407fa80fce *help/getAnnotation+2CAnnotParam-method.html
54eaf7a19db204f5e337d4407fa80fce *help/getAnnotation.html
3d72a83d47676f929cbf855a1fdd2e4b *help/getBamFileList+2Ccharacter+2Ccharacter-method.html
3d72a83d47676f929cbf855a1fdd2e4b *help/getBamFileList+2Ccharacter+2Cmissing-method.html
3d72a83d47676f929cbf855a1fdd2e4b *help/getBamFileList.html
ec6c36e239ab7d422515266846a8c2e3 *help/islandCounts+2CRNAseq-method.html
ec6c36e239ab7d422515266846a8c2e3 *help/islandCounts.html
d08a96feee0d1a89c6b8470ce0d4b657 *help/knownOrganisms-defunct.html
8dbf20b979652441c6a37d46a6b8c54d *help/knownOrganisms.html
2761e23515509397489d6738ea8a4450 *help/librarySize+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/librarySize+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/librarySize+3C-.html
2761e23515509397489d6738ea8a4450 *help/librarySize.html
2779c661f4da8a9996eab3d8c01cd994 *help/nFilter.html
2d54f6b9d1fa209b666043405ee691bb *help/naPositionFilter+2CSRFilter-method.html
2d54f6b9d1fa209b666043405ee691bb *help/naPositionFilter.html
8dbf20b979652441c6a37d46a6b8c54d *help/organismName+2CRNAseq-method.html
8dbf20b979652441c6a37d46a6b8c54d *help/organismName+3C-+2CRNAseq-method.html
8dbf20b979652441c6a37d46a6b8c54d *help/organismName+3C-.html
8dbf20b979652441c6a37d46a6b8c54d *help/organismName.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/paired+2CBamParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/paired+2CRnaSeqParam-method.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/paired.html
3aa4c20282383ec164666ff542c4f425 *help/parallel+20additional+20methods.html
3aa4c20282383ec164666ff542c4f425 *help/parallel-methods.html
3aa4c20282383ec164666ff542c4f425 *help/parallelize+2CBamFileList+2Cfunction-method.html
3aa4c20282383ec164666ff542c4f425 *help/parallelize+2CGRangesList+2Cfunction-method.html
3aa4c20282383ec164666ff542c4f425 *help/parallelize+2Clist+2Cfunction-method.html
3aa4c20282383ec164666ff542c4f425 *help/parallelize+2Cvector+2Cfunction-method.html
3aa4c20282383ec164666ff542c4f425 *help/parallelize.html
83b7643cb85e11c6a7ce53b135ab7565 *help/paths.rds
6732a96df64feada11b0a79991a2816b *help/plotNormalizationFactors+2CDGEList+2Ccharacter+2Ccharacter-method.html
6732a96df64feada11b0a79991a2816b *help/plotNormalizationFactors.html
bcbb864a8d26ef975c0aac3aac24c213 *help/precision+2CRnaSeqParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/precision.html
19d63aac4373f033bd5f6a50edd2e727 *help/print+20methods.html
19d63aac4373f033bd5f6a50edd2e727 *help/print+2CAnnotParam-method.html
19d63aac4373f033bd5f6a50edd2e727 *help/print+2CBamParam-method.html
19d63aac4373f033bd5f6a50edd2e727 *help/print+2CRNAseq-method.html
19d63aac4373f033bd5f6a50edd2e727 *help/print+2CRnaSeqParam-method.html
19d63aac4373f033bd5f6a50edd2e727 *help/print-methods.html
19d63aac4373f033bd5f6a50edd2e727 *help/print.html
a2fb3028e3257aff79e7eadbc126088a *help/ranges+2CRNAseq-method.html
a2fb3028e3257aff79e7eadbc126088a *help/ranges.html
2761e23515509397489d6738ea8a4450 *help/readCounts+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readCounts+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readCounts+3C-.html
2761e23515509397489d6738ea8a4450 *help/readCounts.html
2761e23515509397489d6738ea8a4450 *help/readCoverage+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readCoverage+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readCoverage+3C-.html
2761e23515509397489d6738ea8a4450 *help/readCoverage.html
2761e23515509397489d6738ea8a4450 *help/readIslands+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readIslands+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readIslands+3C-.html
2761e23515509397489d6738ea8a4450 *help/readIslands.html
2761e23515509397489d6738ea8a4450 *help/readLength+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readLength+3C-+2CRNAseq-method.html
2761e23515509397489d6738ea8a4450 *help/readLength+3C-.html
2761e23515509397489d6738ea8a4450 *help/readLength.html
50770759dfaa7949563225279fa89f9e *help/reduce+2CRNAseq-method.html
50770759dfaa7949563225279fa89f9e *help/reduce.html
2761e23515509397489d6738ea8a4450 *help/seqnames+2CRNAseq-method.html
2a304d01e83640e386e0e7182e3d094e *help/show+20methods.html
2a304d01e83640e386e0e7182e3d094e *help/show+2CAnnotParam-method.html
2a304d01e83640e386e0e7182e3d094e *help/show+2CBamParam-method.html
2a304d01e83640e386e0e7182e3d094e *help/show+2CRNAseq-method.html
2a304d01e83640e386e0e7182e3d094e *help/show+2CRnaSeqParam-method.html
2a304d01e83640e386e0e7182e3d094e *help/show-methods.html
a0f90f3a520473f86883d6238462b9bb *help/simpleRNASeq+2CBamFileList+2CRnaSeqParam-method.html
a0f90f3a520473f86883d6238462b9bb *help/simpleRNASeq.html
50770759dfaa7949563225279fa89f9e *help/strand+2CRNAseq-method.html
50770759dfaa7949563225279fa89f9e *help/strand+3C-+2CRNAseq+2CANY-method.html
50770759dfaa7949563225279fa89f9e *help/strand+3C-+2CRNAseq-method.html
50770759dfaa7949563225279fa89f9e *help/strand+3C-.html
50770759dfaa7949563225279fa89f9e *help/strand.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/strandProtocol+2CBamParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/strandProtocol+2CRnaSeqParam-method.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/strandProtocol.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/stranded+2CBamParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/stranded+2CRnaSeqParam-method.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/stranded.html
ec6c36e239ab7d422515266846a8c2e3 *help/transcriptCounts+2CRNAseq-method.html
ec6c36e239ab7d422515266846a8c2e3 *help/transcriptCounts.html
46042271dfcfa084e2687ba110b7163d *help/tutorialData+2CANY-method.html
46042271dfcfa084e2687ba110b7163d *help/tutorialData.html
1e9d19dde28d60257f9ae26baebd5e20 *help/type+2CAnnotParam-method.html
9abe592b9f3ebffef876240ce40ea3e6 *help/type+2CGenome_intervals-method.html
2779c661f4da8a9996eab3d8c01cd994 *help/type.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/unsafeAppend+2CGAlignments+2CGAlignments-method.html
8b6cc57958f34a3924bbabdea3c8d1f2 *help/unsafeAppend.html
1ba36bc2a14615c93b5e613f7c7e8192 *help/validate+2CBamFile-method.html
1ba36bc2a14615c93b5e613f7c7e8192 *help/validate+2CBamFileList-method.html
1ba36bc2a14615c93b5e613f7c7e8192 *help/validate.html
46042271dfcfa084e2687ba110b7163d *help/vignetteData+2CANY-method.html
46042271dfcfa084e2687ba110b7163d *help/vignetteData.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/yieldSize+2CBamParam-method.html
bcbb864a8d26ef975c0aac3aac24c213 *help/yieldSize+2CRnaSeqParam-method.html
6c86dbbfc3a0b57a01b545cf98255b93 *help/yieldSize.html
f95e85e07f9c0a597869df86752d23b6 *html/00Index.html
3a93ac6531c5a6b40b0085f4a675cf9a *html/BiocFileCache-methods.html
8cb6f01b01fab079ee20812166c9098a *html/GenomicRanges-methods.html
e20310dcdfafdcdc9888de761ca5e163 *html/IRanges-methods.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
ce2c22b4202c07a794421b2e6c6a83d3 *html/Rsamtools-methods.html
a9073775bfe6ff0db0524f3fa08ae888 *html/ShortRead-methods.html
d742dccebf3a0b49e80e1aabc8a56bce *html/basename-methods.html
800383572c120ecc0b38cb05b01e69ef *html/easyRNASeq-AnnotParam-accessors.html
93ef2e3bc36e0966abff92b2ec3310a6 *html/easyRNASeq-AnnotParam-class.html
f071ba5cd674c7485ab4204101745a91 *html/easyRNASeq-AnnotParam.html
b3f80c37fdabbfa3a6f5ee35d1d8e598 *html/easyRNASeq-BamFileList.html
26baebf03c12abd705d0cb8d1f9c45dd *html/easyRNASeq-BamParam-accessors.html
e9e1dac1a66bfff47c2ea2dae367b01a *html/easyRNASeq-BamParam-class.html
efdf560f92424ea4f31bbd693ad2a9af *html/easyRNASeq-BamParam.html
275d6c886396caec7505c7ae9d4bc249 *html/easyRNASeq-RnaSeqParam-accessors.html
c83c20fa876bbfe7330b27b98c150de7 *html/easyRNASeq-RnaSeqParam-class.html
30c37ee919f476accdf7eefeb98b4075 *html/easyRNASeq-RnaSeqParam.html
2e962d84a629510e2932fd19e257f11e *html/easyRNASeq-accessors.html
8579b12b1f7ecbba01ea6ff4e679320d *html/easyRNASeq-annotation-internal-methods.html
52f0ac8992e284060115198461451591 *html/easyRNASeq-annotation-methods.html
0f08432ddf37a10bb69736607ba57e0e *html/easyRNASeq-class.html
677c78b6c104c98f37b7888056cc6e73 *html/easyRNASeq-correction-methods.html
a311ad2c041d7f3e601b0eb221e8840b *html/easyRNASeq-coverage-methods.html
1906d18b9dd5ff31658f646ad5336b61 *html/easyRNASeq-datasets.html
cf76ab18435357a5ee70cc62fd8b1927 *html/easyRNASeq-defunct-annotation-methods.html
ae67f541e0298991abbfb82b7439d0ff *html/easyRNASeq-defunct.html
da10902e60a2d2b9897f2137d67ae868 *html/easyRNASeq-easyRNASeq.html
be323f740c8feda1a5ca852c8a323770 *html/easyRNASeq-global-variables.html
3213fd7dcb36b21df003df8e64ff304a *html/easyRNASeq-internal-AnnotParam-methods.html
6ddadb9a505a184e4d814492baec61e6 *html/easyRNASeq-internal-methods.html
01f4d0a8d70b83c72b9f786187114f64 *html/easyRNASeq-island-methods.html
63bbc4402bb4b0ad3847fda2035475d5 *html/easyRNASeq-package.html
f479def738db4f986a60d90e7441aa0b *html/easyRNASeq-simpleRNASeq.html
e2d06a20dbdbc235d17813418b2e1e2d *html/easyRNASeq-summarization-internal-methods.html
e46233a3dc6f1fc16bf917414de704a4 *html/easyRNASeq-summarization-methods.html
317efa48d428bc1d0bf6cefac28f0f40 *html/easyRNASeq-synthetic-transcripts.html
ce39ba86db67f8249648eb24ff9366b4 *html/edgeR-methods.html
f32214b788831f09e5678494d9075743 *html/file.exists-methods.html
aeff30c31ef085b143c8aa5354030b70 *html/genomeIntervals-methods.html
247569e134474fe561c933bd3165aead *html/parallel-methods.html
c549f5ed6010fedd525368e71c2a82ea *html/print-methods.html
9ef9781f840313238d1f6a9c2c2be500 *html/show-methods.html
e275ee343d67e1f8d981696349c594c9 *unitTests/test_accessors.R
16fbcedb31013db806ceb9f61b5b2370 *unitTests/test_annotations.R
e9e3de373f9106c5ad6cb9dddfd95c37 *unitTests/test_classes.R
2b71b7c86107e6f7b1e6580a2ea06a6f *unitTests/test_extensions.R
ba477114ab84cf27cf373e0ee6dd22ef *unitTests/test_methods.R
1de176bc55da0d3f0829b442c67f4f97 *unitTests/test_print.R
2ad9f3b5dc8c22559d5ee4d0325f6fb2 *unitTests/test_ranges.R
ffe5c92cacb8233e7fb7c4294488f00a *unitTests/test_variables.R
