29741725acb73998a9205dd69963d0d4 *DESCRIPTION
d51d604bcc5b962495c10001ca160e7a *NAMESPACE
1cef876003267254fdc87746da4f3a87 *R/ClassDefinitions.R
7928a2b8066730b70ff0a4d03d25bf05 *R/GenericDefs.R
6a7123cc2ac972ad6bb6a4ee8e6e5438 *R/asymmetryCheck.R
86280c9cd27327c9ac4379cc8615dc1e *R/calcDenovo.R
545c6038281994dd092eb9f386f89992 *R/calcExp.R
1205b9d26cc7c281073dfb09ce49fdc1 *R/casperVignettes.R
8668266ad63dd7f89f41c95ecae67064 *R/checks.R
e6e531e90ce58b78708889be1d494b6a *R/createDenovoGenome.R
de44bb3ce8ecf204719a873e8de463d2 *R/denovoExpr.R
e858f7b29bcfa5fe9cff9f2621e26ed7 *R/genePlot.R
fbbe4d39dbc9032c7b345d55c984a65a *R/getDistrs.R
e9c0d41854ccfbeffa8abe4245b6ca38 *R/getRoc.R
e38fd52b402e72010d49c125b61ff497 *R/makeTranscriptDbFromGFF.R
1eb07297ba5b5976159fe558e3d2284d *R/mergeBatches.R
14cd52f433e7f070b5d33acde8c395c0 *R/mergeExp.R
204ed718a41403d70cdccde386377ec3 *R/modelPrior.R
cda8c17670da877a8c9e627c77af954a *R/pathCounts.R
de42c316f50295045ff4027e18403550 *R/probNonEquiv.R
2fe3de9ab2f28ddff714ee4b26bb7075 *R/procBam.R
a55baffb5783b714a92fc27f799771e4 *R/procGenome.R
2eb94a98ccde9c20027c2ef9b7f2a3ce *R/qqnormGenomeWide.R
01d132026dd9ad0bcce1c8b9f66e6d1b *R/relexprByGene.R
ff4c1929a2b4b96a664fb356f69652ef *R/rmShortInserts.R
ba9080fdbc7c0b56d8845896fe0e9cd8 *R/simMultSamples.R
729afdaa88fb91072654e488448499bf *R/simPost.R
ccd6d27fb012e9313cbff259650f51bc *R/simReads.R
8872afcde287d0dcca13e034e3acbba6 *R/splitGenomeByLength.R
68b2dddce337b1ba23b1c570c6132edf *R/truncnorm.R
76c150c983adff33e93e1837f83fd0af *R/wrapDenovo.R
d58e5b3ccce81d1f9f2c7329c254d60d *R/wrapKnown.R
75843f24483932462288470b0548f6e7 *build/vignette.rds
affb6c3bf508631c9fa5c5fa7956cd07 *data/K562.r1l1.RData
a52db54423e8a50fbf63c9783833b8ed *data/datalist
f194f21f49de34b758c67b7277cda932 *data/distrsGSE37704.RData
8dee49102ebdcec8940fdca0fe4e94df *data/hg19DB.RData
88a7c05692569d76a7434218f632c75a *inst/CITATION
d2c47e2f91bf3ab02318392999d9bbb4 *inst/doc/DesignRNASeq.pdf
ab6ef8d34a5d09720c4cc995b2320fdf *inst/doc/casper.R
45115d9e1d94eb7923be040398d24a4d *inst/doc/casper.Rnw
55e2fa4eb348252d43de430e22f54889 *inst/doc/casper.pdf
4caf1daf9cf80aefa30ebacf3ebadf40 *man/K562.r1l1.Rd
436fc3cdc85c28834a441bdfb3ae21cb *man/annotatedGenome-class.Rd
33cfc29aebdb33579bde00b436d451eb *man/asymmetryCheck.Rd
78d9c09627a84246161dd9a25cd0e650 *man/calcDenovo.Rd
087c97ef7390cf07b465726a28057966 *man/calcExp.Rd
fd34cbab8053f5d48030668f9ed85809 *man/denovoExpr.Rd
3d0d24c48a3e264139d65363be7e59a0 *man/denovoGeneExpr-class.Rd
9c710f39d6bf568fb60d71f46d7b4fc7 *man/denovoGenomeExpr-class.Rd
6f3219c0e7a9c12949a49a434e56e9de *man/distrsGSE37704.Rd
432d4c9807125978c45f3871ba06e1d7 *man/genePlot.Rd
fe183214938f12df8fda44829dab4425 *man/getDistrs.Rd
f061f1c099ec93a37b5404d8deeb406b *man/getIsland.Rd
c89b170e6fe0ef413f8588fff88c0dd3 *man/getNreads.Rd
d81aae6f3fcbab0d36582c5351c65de6 *man/getReads.Rd
7360e36f7a1a55db249a707d0607134e *man/getRoc.Rd
5aa5fb01196c30881ee2798f2a268a8d *man/hg19DB.Rd
d408d41ce5b62b49bc6091766e822641 *man/mergeBatches.Rd
192e251e4f13e2915b852f9cc62e6e53 *man/mergeExp.Rd
8786961d151cb093f15b9fc49097afe9 *man/modelPrior.Rd
a4267f2b3cf3abadeb1cba1b94e9b0b4 *man/modelPriorAS-class.Rd
01f43e2d4cad50ffa6d1542633bd3198 *man/pathCounts-class.Rd
fa81fec561edc2a5ab2eb1e6cfb3f41e *man/pathCounts.Rd
e9f6a8a6b813a476e64ac98ef10b3a70 *man/plot-methods.Rd
55bb4de65c988d099ffd624e8229ace2 *man/plotExpr.Rd
a552e064ad0fb08a99d48a51025d8e9d *man/plotPriorAS.Rd
a175ffb06fa64bc23cce9807b318e888 *man/probNonEquiv.Rd
eea04b3c418a83398f76a5108cc84917 *man/procBam-class.Rd
52f59fc9954d476095874ab984f4a089 *man/procBam.Rd
f6546e6691b148a46a5aa3cc8fb1e137 *man/procGenome.Rd
bfab5306eda390d49fb1b7a45a1e2424 *man/qqnormGenomeWide.Rd
f2567024004badc121b263eb52a2ad77 *man/quantileNorm.Rd
5c2de7ea873013faecb5f821f696c7b9 *man/relexprByGene.Rd
fca92d74704954a3fb48f80067c13017 *man/rmShortInserts.Rd
2e20d52b7748cff7cde258ee375b773d *man/simMAE.Rd
69ba5e61fd3b87a1418e1f7e575edd84 *man/simMAEcheck.Rd
dbe17b3e6c7afd35fb0912ab33111aea *man/simMultSamples.Rd
6b9ecaaf6e37a8ad670f1125dbe9f3ff *man/simReads.Rd
5eb5a5a14e6df366ba570f86fe9b87d1 *man/simulatedSamples-class.Rd
3f159da997354210c1645984f7cd0e29 *man/splitGenomeByLength.Rd
8f83a5e64cff5d2bb2ebce8402093223 *man/subsetGenome.Rd
ea34f0a8024871a36714821fcbe4cd12 *man/transcripts.Rd
9152caaef263b42001f19ca4f1cc2c19 *man/txLength-methods.Rd
40658ade6606bd1dcc228f25b8b8d225 *man/wrapDenovo.Rd
fd26ccace042ac381f93089a627b8a5b *man/wrapKnown.Rd
a52f6a81a140982d642218c9ddfb49b0 *src/casper.cpp
0c3c46d5ddff97bf06708ce974cd595a *src/casper.h
e447a64899ba594670a4661337f18932 *src/cppmemory.h
013eee42090de5928b1e5fa1475648f5 *src/cstat.cpp
848249211dff2233cc165bbc4e208415 *src/cstat.h
d94e0af64eda4000ba876114c1f32d42 *src/dataframe.cpp
c7d395ba8e81941cb902e79575ff3a4c *src/dataframe.h
a64556df96d7c8f23954a5f54c999c69 *src/discretedf.cpp
fd8220b5c4d3b84e8e355ea67bc5d7f0 *src/discretedf.h
36b45ef46db526d870df024f0e540da7 *src/dropVariant.cpp
fdb4da9c78c2090287944c2668636460 *src/dropVariant.h
8f8dd47f95b7fc8cd26f9f51dc8f50b0 *src/exon.cpp
13f8bde44c2ff3c6ea92f75e21a64c3e *src/exon.h
ff2d7a38db1fce4a8c42a206f8982f45 *src/fragFunc.c
a77051f2ccad65e3e1a17a84c7771388 *src/fragFunc.h
4b21b43d6b4dc647f913f09f99578ad2 *src/fragment.cpp
bad7a3ed2e4783d4495c5f0e491b75b1 *src/fragment.h
993d642c241d046d1589ac1aa9628939 *src/functions.c
e3ea22b2c715c71ba9b5e3aee780e0dd *src/functions.h
5933ce3223ba1da97a8cc467725f2423 *src/hash.c
36edc6e5cdb015ffdf8a5490182191f3 *src/hash.h
35101ee3a6b27839ad97f8278d042b39 *src/header.h
9f87f4ddb05d48c7a4f6447a075222ba *src/join_exons.c
287b567faaaafb70a79840a52acd93ff *src/makeIslands.c
8747e46751e399aa452542903bb5302c *src/model.cpp
b0507b5a50888dfe9af6f1e66678a0b9 *src/model.h
1b2e1447574c024d5959e5ec880b0f3b *src/model_cmp.cpp
f922fd45af528e721ca39952ee54ad63 *src/model_cmp.h
e077f2b7ef874eb174e463d5b4222261 *src/pathCounts.c
893d2c2f53b0a2d2ba9d49b540bd767f *src/procBam.c
7528b2294f37f31d1bc66026d69298b8 *src/rcasper.cpp
54872ce5a2985e4c04002694833c1408 *src/rcasper.h
dd5d0d07ba1340be083935dad740df07 *src/seppel.cpp
9e2710be41903c471c5fdb8b95e6db2b *src/seppel.h
fafd7c6aa466289e46c307cd1627d576 *src/simReads.c
60cb3881e251b4743ef52bb3290e681f *src/simReadsfunc.c
13ee93a8e567ca8a6ad38b536d4f74f4 *src/simReadsfunc.h
d4827e6b72c35c57e1bbd333bc259a92 *src/smartmodeldist.cpp
ce7108b2aef23fc527e10d78a537013c *src/stdafx.h
c5c630677157ddcd4f0bdb3607cdf3d6 *src/targetver.h
5bebd612235a71b95bb76adf91a7e44a *src/uniqQname.c
3d3b617f0ad6b3eca184ed3bd6fe1eaf *src/variant.cpp
cca05200a1ab368cc32ef0b93808ad1f *src/variant.h
09ff66ec8f87336f268538b9ee0198f1 *src/variant_cmp.cpp
cf31cd4d21bea1f852286c8b41985ad6 *src/variant_cmp.h
3cf70fa1038db7e8af525c13cbf06dd2 *vignettes/auto/casper.el
45115d9e1d94eb7923be040398d24a4d *vignettes/casper.Rnw
34634b586c89e41fe71f0ca39ec6ed4f *vignettes/references.bib
