7933ff54794e93c613e9fe7f0ba40f0b *DESCRIPTION
9b7f33dcc8b31c1dc890b93f6428f778 *NAMESPACE
08fe8d855573a0c8375b8e1337bf61ec *R/AllClasses.R
4720748a0a9b35148ea0f00f2c0c7f9d *R/AllGenerics.R
5dd65c58e3eabc163f9e112ad88c6c0e *R/database-setup.R
ab1b0646eb9d54f555f8b303e35e507c *R/methods-CuffData.R
45add1008134cf96702fb36c046d13c8 *R/methods-CuffDist.R
c562b21399c9d6b744a3ac296e8b0759 *R/methods-CuffFeature.R
e6cf30266255f9fc4c08e0409e626080 *R/methods-CuffFeatureSet.R
af94f17b2aa14759b668ba5d215dc7e1 *R/methods-CuffGene.R
af59b554a98bb091f3391613eb9f979c *R/methods-CuffGeneSet.R
fc468a0a0408aad7e322109437f04c0d *R/methods-CuffSet.R
37af07eafa0a3ba26e049fa63c6a4992 *R/tools.R
3d576b9dda9215c4bddb45ecef965e6c *README
a675e93ebe2fd041ecefc2083a9399dc *build/vignette.rds
95effbbbf6135a883a9cd3fbe1620eb5 *data/sampleData.RData
5efebf5ca08d5c21bf838bc1d6ba8620 *data/sampleData.rda
7740f7b92ec0e9f630fdf49af9e477ae *inst/NEWS
bf4a10b40a15443c91d4e871a923c132 *inst/doc/cummeRbund-example-workflow.R
1cf17ce4c24507288a5272fd72003c6b *inst/doc/cummeRbund-example-workflow.Rnw
1de5fa3a85cadbc93390e670e2d5e8db *inst/doc/cummeRbund-example-workflow.pdf
94d1b0031ce72fe85958a90a355c655d *inst/doc/cummeRbund-manual.R
7a6ad862145751c8231e2153c16c3ee6 *inst/doc/cummeRbund-manual.Rnw
48031c06f2712c3de4b1ff2cb1808547 *inst/doc/cummeRbund-manual.pdf
d750866aa0c9df7b8a2416b605aad636 *inst/extdata/cds.count_tracking
55054b333f3d37b29ec9c8d4ed247a5c *inst/extdata/cds.diff
872cf05900e727e0d71b270d0ff53bea *inst/extdata/cds.fpkm_tracking
bf863abcbbb9eab2b6dc4742ecfa010c *inst/extdata/cds.read_group_tracking
7ea0edf89f0ddc5e834cb5466288d4b1 *inst/extdata/cds_exp.diff
268c5340a737a3c211bcacc1a1c13693 *inst/extdata/chr1_snippet.gtf
b926443705216b33fe2965e730efb46a *inst/extdata/cuffData_schema.sql
8a5e8a2753eba7b6667dbe215a248fee *inst/extdata/gene_exp.diff
af41baca8b3e26509452c2436d234d65 *inst/extdata/genes.count_tracking
145fd3994f9648d5ada1d604e24c365c *inst/extdata/genes.fpkm_tracking
c563202c95aa9aeaa08e4bf759a77df5 *inst/extdata/genes.read_group_tracking
6157f98d3b7081152fcad9898a970a74 *inst/extdata/isoform_exp.diff
d26a4ce41f3537165f5ec8720005fb5e *inst/extdata/isoforms.count_tracking
3df37bd586fc05d216f551cdb8a25ff8 *inst/extdata/isoforms.fpkm_tracking
732428dd0ee431d16139debde986a780 *inst/extdata/isoforms.read_group_tracking
05a7e6754b834b16efeab5f32b761338 *inst/extdata/promoters.diff
5504299772cc9202185abcb03fa8c31c *inst/extdata/read_groups.info
4302c47866e67a5ccb87015bb4cfad4b *inst/extdata/run.info
76743810e9158eadc8454d59bd2fb5e1 *inst/extdata/splicing.diff
2ad3e5a485eba94a838bac21160715f5 *inst/extdata/tss_group_exp.diff
d52d7fac3419d9e4158faa8972302c2f *inst/extdata/tss_groups.count_tracking
5f6fcb9d599665971639f3b53dc40a54 *inst/extdata/tss_groups.fpkm_tracking
dd6e1ea022372357ee00868068b80586 *inst/extdata/tss_groups.read_group_tracking
c418b300973b33a65f28926ad1846a8f *inst/reports/runReport.Rmd
ad6fede4ef3b243e7f08843092030886 *inst/reports/styles/report_style.css
6688987e2ebe353c4cd9d4c3b9c26e3d *man/CuffData-class.Rd
5f2ef5802833ca7333985ef8a57e418f *man/CuffDist-class.Rd
b676dfb8d2e7b3a25f9be572559ef917 *man/CuffFeature-class.Rd
2d54316326a31f7610788de78dee0c3c *man/CuffFeatureSet-class.Rd
82bd4f34b495d382e72b7620392ee9c1 *man/CuffGene-class.Rd
ec8d7f8a8623376b008b21978dab6799 *man/CuffGeneSet-class.Rd
d94152a5e8a29546a472dcb895f19d77 *man/CuffSet-class.Rd
5a2f4c2fc94a9200f546abeb95eda164 *man/JSdist.Rd
8cac089d34e79774a2c491434e79c0c7 *man/JSdistFromP.Rd
11f6207c362e4be6967d326a122ea286 *man/JSdistVec.Rd
12e08aaeae5b8b14f1059fc329a6d05f *man/MAplot.Rd
6932d51e4c947c933769951cf13f9471 *man/PINK1.Rd
cf676d4852da9d91794fc625ff3d662b *man/QCplots.Rd
ad1bd7dad6045f5521ca032da849be05 *man/addFeatures.Rd
17d1790758e29c5d11f517d6bb8f469f *man/count.Rd
c0d444848f4adb9a6be817321bf975e2 *man/countMatrix.Rd
f9d640113ed1349e0b3a9781d239d081 *man/csBoxplot.Rd
523a0a3d4f773486b97c353265a8c6ba *man/csCluster.Rd
0aa563a1f0d6228c5a45c859f43ec0ce *man/csClusterPlot.Rd
80c8ea974a31d1db1bd928991c4a458a *man/csDendro.Rd
94c53c9f22a97061879acbfdb7480bd7 *man/csDensity.Rd
883d95101bb26f04e7e14811b362aa38 *man/csDistHeat.Rd
77423dd27531ff264891b45fcf704512 *man/csHeatmap.Rd
2f42e4bdbbbbc62adf279a53bec72a8c *man/csScatter.Rd
9e6084c4af354ef12b99263185050dd5 *man/csSpecificity.Rd
49ab49e659742aaf24e1654ba9dc163a *man/csVolcano.Rd
470857918af65b7b203290a0e36bcf24 *man/cummeRbund-package.Rd
51451cb97c33ecf4c9e36dc7d0925622 *man/diffData.Rd
09f6171f434a9a840523eacd84108283 *man/dimensionality.Rd
24d1974f9d53741925928c4fd5850b71 *man/dispersionPlot.Rd
6d43d0db06abefb127dc9330e51d8913 *man/distValues.Rd
2357a9dcaf7b2df3042f62b192f8d6fa *man/exploratory.Rd
c5c83497e9e46ee62a595d5f285983a1 *man/expressionBarplot.Rd
f8930e1509026e45f4ad3eb52bf7ad8d *man/expressionPlot.Rd
e93f3fcb1be69933e3e27bc13d1fb6cf *man/featureNames.Rd
457debfa096da683db1652c2b9145bed *man/features.Rd
8323cdab215a4dd53d8e93a07854492e *man/findGene.Rd
58eed0482db12de89fe3ec775301d113 *man/findSimilar.Rd
bba0a7778e92630462b41124852b6b13 *man/fpkm.Rd
412156711371759f1adfb6d685b575de *man/fpkmMatrix.Rd
5dbb1edc03e51ab8401073ce89b1a5b2 *man/getFeatures.Rd
e5b52982b1904b32ff58ffd6d3a40c4e *man/getGene.Rd
1a0400ee64ffa929922bb2aac81962f2 *man/getGeneId.Rd
62560ef2e0b4bcae8470c880e5d51c93 *man/getGenes.Rd
e48174fa516b59ee2c42294bbbac5a49 *man/getLevels.Rd
a0a110e17a599acc9051379c298f8d1f *man/getRepLevels.Rd
542a19898788cca6ccbf0c6e999d4261 *man/getSig.Rd
c5e762c89f506979123e3f5fb2f2e1d8 *man/getSigTable.Rd
2ba064a0a6aba058082e5a049331b45a *man/makeprobs.Rd
60e542342ce77a6f399c544e9aebd00a *man/makeprobsvec.Rd
e11058e805de375c19daad336f8c17fb *man/readCufflinks.Rd
650606515fec0edd5274eda0490e3919 *man/repFpkm.Rd
6a12f8003c5019c418199a115d6ff26f *man/replicates.Rd
69e5ab835ef7f70dff6cc81f3b466b76 *man/runInfo.Rd
81abd5176e4644c4fc1d6dfb6b48dc5b *man/sampleGeneSet.Rd
e71f4c8843a2adc0f07aadc1d85d6b3c *man/sampleIDs.Rd
24ce9e1001d3ac1fb90c8b6146bb3d41 *man/samples.Rd
c0aad4a3388ddb9f823fdbc43d46263d *man/shannon.entropy.Rd
69cd7f12140eed73a169fe40d0d81149 *man/sigMatrix.Rd
47cd8deb604624196a30cf60abf12bc5 *vignettes/ENCODE_SCV.pdf
ebcb935dba061978418ebae0aa4a7392 *vignettes/cuffData_schema.pdf
1cf17ce4c24507288a5272fd72003c6b *vignettes/cummeRbund-example-workflow.Rnw
7a6ad862145751c8231e2153c16c3ee6 *vignettes/cummeRbund-manual.Rnw
