7236e2079163543fc508e1eb1ec4d46b *DESCRIPTION
0ccefa733046bad88be8f6309850f0da *NAMESPACE
0b296c1be50d387730e8908420ba04a4 *R/Script_PLATE_01_CREATE_MARVEL_OBJECT.R
af1834efb22726cd255ea08ded0f1894 *R/Script_PLATE_02_COMPUTE_PSI_0_Compute.R
512c66107e144d58b79b958b572e3606 *R/Script_PLATE_02_COMPUTE_PSI_1_Compute_SE.R
5e8e814a6d061d19fd5551b39ce5b279 *R/Script_PLATE_02_COMPUTE_PSI_2_Compute_MXE.R
4a57291c19dbb93af7e58e4fa5e1cd9e *R/Script_PLATE_02_COMPUTE_PSI_3_Compute_A5SS.R
18b307b3ccb8cd71edbc0f7b2c7f0d2d *R/Script_PLATE_02_COMPUTE_PSI_4_Compute_A3SS.R
bec02f53ffee75d8e135378f0730ede4 *R/Script_PLATE_02_COMPUTE_PSI_5_Compute_RI.R
b2058efd848f193278be762f9890a608 *R/Script_PLATE_03_PREPROCESS_2_0_SubsetSamples.R
a61fcfe6603cd4a3462c7bb17cf1a9c8 *R/Script_PLATE_03_PREPROCESS_2_1_SubsetSamples_PSI.R
24ea811ff267d0a58811d0b9b138d29a *R/Script_PLATE_03_PREPROCESS_2_2_SubsetSamples_Gene.R
20cebbb6d5e51de68a6d2856eddd982d *R/Script_PLATE_03_PREPROCESS_3_0_CheckAlignment.R
fac1d5f1fdd617c575a036bc90ebb332 *R/Script_PLATE_03_PREPROCESS_3_1_CheckAlignment_PSI.R
b6af41f190d28507140595c91da25170 *R/Script_PLATE_03_PREPROCESS_3_2_CheckAlignment_Gene.R
4becda6bf72eb6ed909c2e37638bb009 *R/Script_PLATE_03_PREPROCESS_3_3_CheckAlignment_PSI_Gene.R
62c9e59f7d017f3ba234f04dbf14e849 *R/Script_PLATE_03_PREPROCESS_3_4_CheckAlignment_SJ.R
f8c4c6df6eec89c2ea822a242d69c8c6 *R/Script_PLATE_03_PREPROCESS_4_TransformGeneValues.R
7265a6b146684f3f9eb8338aeda5ce61 *R/Script_PLATE_04_MODALITY_ANALYSIS_1_AssignModality.R
332203cfb7b7f66a24c9a9bb6b04eba2 *R/Script_PLATE_04_MODALITY_ANALYSIS_2_0_PropModality.R
da891a3d18dad8223ce64d636978dbe0 *R/Script_PLATE_04_MODALITY_ANALYSIS_2_1_PropModality_Doughnut.R
ced9273a6ce8aa34f1f589d5326db74a *R/Script_PLATE_04_MODALITY_ANALYSIS_2_2_PropModality_Bar.R
945c0f6598765b16bf710ba39fb4a971 *R/Script_PLATE_05_PCA_0_RunPCA.R
dfad165be1357a5fa5db6dd763ec56a3 *R/Script_PLATE_05_PCA_1_RunPCA_PSI.R
32b2a017b638a095650a9af4c87152fe *R/Script_PLATE_05_PCA_2_RunPCA_Exp.R
41ba3a8946c435c0ecf01169ae0c4abf *R/Script_PLATE_06_DE_1_0_CompareValues.R
b88ab77e1244a1645ff24cf343998b17 *R/Script_PLATE_06_DE_1_1_CompareValues_PSI.R
49a241d0820ded28ae26e194eb475e14 *R/Script_PLATE_06_DE_1_2_CompareValues_Exp.R
70d881d9fe434ab1fe60940beb732071 *R/Script_PLATE_06_DE_2_0_PlotDEValues.R
6974b99c8f7920c6b00540cb2c512292 *R/Script_PLATE_06_DE_2_1_PlotDEValues_PSI_Mean.R
abd0bd470b1ce28017a3e35a23b4b91c *R/Script_PLATE_06_DE_2_2_PlotDEValues_PSI_Distance.R
3dc379b48b2c50b83f31a0b86fa554ee *R/Script_PLATE_06_DE_2_3_PlotDEValues_Exp_Mean.R
8948b1329f9205f5bac7c0a335725e78 *R/Script_PLATE_06_DE_3_IsoSwitch.R
6b90311a8d53ce83f07d230c455fc9d0 *R/Script_PLATE_06_DE_4_ModalityChange.R
cbf80716c266349053953f8690c1901f *R/Script_PLATE_06_DE_5_1_GO.R
d54c5da65e07e5bd29063dc6767becdf *R/Script_PLATE_06_DE_5_2_GO_Plot.R
56fd50a03008fd66be49ae6900c4cf88 *R/Script_PLATE_07_PREDICT_NMD_1_ParseGTF.R
5e3d0602b0cba337f185dd7b93542657 *R/Script_PLATE_07_PREDICT_NMD_2_0_FindPTC.R
f3fad80f3c8bd6de2f7aa704647d01b1 *R/Script_PLATE_07_PREDICT_NMD_2_1_FindPTC_SE_PosStrand.R
b76f278d3993ed39ca8f068df35f84de *R/Script_PLATE_07_PREDICT_NMD_2_2_FindPTC_SE_NegStrand.R
a64dc8083965b18f3db2dc70f11de547 *R/Script_PLATE_07_PREDICT_NMD_3_1_FindPTC_RI_PosStrand.R
bfa165117e0dd31de83b4cde3f8309ea *R/Script_PLATE_07_PREDICT_NMD_3_2_FindPTC_RI_NegStrand.R
fbec14520db0ef03526c1179ac305dc3 *R/Script_PLATE_07_PREDICT_NMD_4_1_FindPTC_A5SS_PosStrand.R
7f3626eca1370eab6a0f5732adb9140d *R/Script_PLATE_07_PREDICT_NMD_4_2_FindPTC_A5SS_NegStrand.R
02e5885df91a1e5be45683f1b027579b *R/Script_PLATE_07_PREDICT_NMD_5_1_FindPTC_A3SS_PosStrand.R
993abac9b588ce9c0297a0987fe9cb63 *R/Script_PLATE_07_PREDICT_NMD_5_2_FindPTC_A3SS_NegStrand.R
e67119ec0327ef86d0850b480e2ce72d *R/Script_PLATE_07_PREDICT_NMD_6_PropPTC.R
2cb70960e51cb4a32acf348455556e52 *R/Script_PLATE_07_PREDICT_NMD_7_CompareExpr.R
49bce73825f4ee99abd838cd71f9e8a9 *R/Script_PLATE_07_PREDICT_NMD_8_AnnoVolcanoPlot.R
0591333bb87e0a1c7e011479feb31ea1 *R/Script_PLATE_08_ADHOC_PLOT_0_PlotValues.R
7368cf8f06f75b9660bf40f58ab38ae1 *R/Script_PLATE_08_ADHOC_PLOT_1_PlotValues_PSI.R
008ec5402dda940fb2f69a88846dc1f7 *R/Script_PLATE_08_ADHOC_PLOT_2_PlotValues_Exp.R
2d8becd5cfdf99359b039b79f0e3a3b5 *build/vignette.rds
5574abca249b53be6ddd5b7728474f2d *inst/doc/MARVEL.R
d18d908e45697d2337098fc0c611df52 *inst/doc/MARVEL.Rmd
3982176a5ce4b274bfe8acc6ae78fc8c *inst/doc/MARVEL.html
9955708de1d4d7a2d8538269721bc199 *inst/extdata/Cover_Figure.png
d16ce37d23651339d09d5fd024ce82d3 *inst/extdata/Data/A3SS.txt
7c38a921bd8af5a58e960cae98a01814 *inst/extdata/Data/A3SS_featureData.txt
f47325eafe71f93d44299aab9fa046c6 *inst/extdata/Data/A3SS_featureData_Validated.txt
109a3619fc56621845fd9655ece23cf5 *inst/extdata/Data/A5SS.txt
91321c5aee34362d0e6f396f3d9abaa0 *inst/extdata/Data/A5SS_featureData.txt
aafd5bd4ba765e307efd444ee2c60528 *inst/extdata/Data/A5SS_featureData_Validated.txt
bafe216daf594eddad622a1d3ae4c63a *inst/extdata/Data/Counts_by_Region.txt
1aa25c77f23a0fa7c5044ec36fe91ea9 *inst/extdata/Data/MXE.txt
44bba2e957355b7f382a0482ced73013 *inst/extdata/Data/MXE_featureData.txt
a3610f97eab73741fc6a039534128460 *inst/extdata/Data/MXE_featureData_Validated.txt
ca3294a5886f1bf3259e03b572d3436d *inst/extdata/Data/MarvelObject.rds
005f97aa0d689619b3552aa69167e1a8 *inst/extdata/Data/RI.txt
260c3b002f6956c632ddc83551f5d692 *inst/extdata/Data/RI_featureData.txt
40cd55177f62b7dbfcf98cc63b172f81 *inst/extdata/Data/RI_featureData_Validated.txt
c76514dfec84d905d738c4218f82b563 *inst/extdata/Data/SE.txt
9b880b41602d567ea8ba6d558fe56776 *inst/extdata/Data/SE_featureData.txt
2adc7966bfd20bc6d2ddd4abb169e5f8 *inst/extdata/Data/SE_featureData_Validated.txt
18bb9922f8b7e522eff3ce4f48d2ac7a *inst/extdata/Data/SJ.txt
aa94148ffc00346fce9cdf003e98f4bc *inst/extdata/Data/SJ_phenoData.txt
3f9c0bbb36523e4e6985edf6edd27f98 *inst/extdata/Data/TPM.txt
6969c173c08c66de7708a796e280c831 *inst/extdata/Data/TPM_featureData.txt
aa94148ffc00346fce9cdf003e98f4bc *inst/extdata/Data/TPM_phenoData.txt
035c6a33bfcc5fbafd93a99c45af4e6b *inst/extdata/Data/gencode.v31.annotation.gtf
a9b0aa3e565916e86a88414ab2c75d63 *man/AnnoVolcanoPlot.Rd
0a6874436df1634629936deff0857e91 *man/AssignModality.Rd
05b97dd9a61b00ae314e306fe5df01d9 *man/BioPathways.Plot.Rd
e7e008e3f8a5ddb76bc9f0dfc78f4e27 *man/BioPathways.Rd
782937e1bfa66f9539bd98366b2e37ab *man/CheckAlignment.Exp.Rd
9aae81b93fb0df3e88046e307cc74a82 *man/CheckAlignment.PSI.Exp.Rd
f44c5a343703f1947a42eeb7f7db0239 *man/CheckAlignment.PSI.Rd
cfada1a9c59ee12a9228a53c17344fa9 *man/CheckAlignment.Rd
87292433d771779cd126b55d6202d667 *man/CheckAlignment.SJ.Rd
f59a721345cead0b07cd94399666a027 *man/CompareExpr.Rd
cef1179b2b81687b3671a8ad563e36e7 *man/CompareValues.Exp.Rd
2e03608a90638b992347003cad32db04 *man/CompareValues.PSI.Rd
87fef0fb3af87e14a06667f9280f0588 *man/CompareValues.Rd
f3b731bc35f328e46afe07c9f5e576fe *man/ComputePSI.A3SS.Rd
ac2f132b0c6fe1681d152fb936129e81 *man/ComputePSI.A5SS.Rd
018ce4caf6ac38e0db6e5d39476a3b05 *man/ComputePSI.MXE.Rd
2b8f075052c04b82c5601590616fce73 *man/ComputePSI.RI.Rd
7acad06594af3c439ccd0aa4b1dc6a46 *man/ComputePSI.Rd
4340fbf3aba328306134aa8f09a8e5b2 *man/ComputePSI.SE.Rd
2f43f043ad51cb880f8ca1e85ae11765 *man/CreateMarvelObject.Rd
9a95ffd2f0d8d5054ee3d5014658f5bc *man/FindPTC.A3SS.NegStrand.Rd
4350e78948fc7e33a567327658120dc9 *man/FindPTC.A3SS.PosStrand.Rd
7c3bae4ce89ead896c151a060cd99cfa *man/FindPTC.A5SS.NegStrand.Rd
e62bff1f2252e09a9a64e6a02dbc3a31 *man/FindPTC.A5SS.PosStrand.Rd
adca23bfa7b70807d9e90d74e07a8458 *man/FindPTC.RI.NegStrand.Rd
35c92303c61e61b8ae7137ae36e23bb5 *man/FindPTC.RI.PosStrand.Rd
30af31e5b21726cac46bd2110fc16146 *man/FindPTC.Rd
4482fdcea4cb78a05205b1c6ac6f882c *man/FindPTC.SE.NegStrand.Rd
749f67ec21dd029ddbc31eb123478fbe *man/FindPTC.SE.PosStrand.Rd
7ce8bddf1cb4ce62a4414df1bc6791f3 *man/IsoSwitch.Rd
74bc56d60f1ae756b9222fbfdca14838 *man/ModalityChange.Rd
62e8f8cc823403cc90b78afdd606c0da *man/ParseGTF.Rd
b07f4e336d57cfee321fa34a82de338d *man/PlotDEValues.Exp.Rd
eefcbad9e441cfe24e83b31197d34d46 *man/PlotDEValues.PSI.Distance.Rd
0a633f0fe1ddb1d4b78043d8547533f3 *man/PlotDEValues.PSI.Mean.Rd
fc5883736c41a90c66ec07bdd3cbb8a2 *man/PlotDEValues.Rd
9fc2fca17febabb4ee4a89f808353090 *man/PlotValues.Exp.Rd
fcfaecdaffab0ec992eb2743bbe11651 *man/PlotValues.PSI.Rd
9d5b7ad9fd316076d2e722f2dc6be87b *man/PlotValues.Rd
d2536c95d038f053f714d18f87be5480 *man/PropModality.Bar.Rd
1e8dfa28da957e5475f488a62ac2c668 *man/PropModality.Doughnut.Rd
efdbe97530dbcaa9668159bee8c2bb86 *man/PropModality.Rd
5d5e52ca3e48b285221187e223be9919 *man/PropPTC.Rd
2d625da836a26b462163627f0c032d16 *man/RunPCA.Exp.Rd
337f60a9dc6c368fe9679b27530d8c26 *man/RunPCA.PSI.Rd
e9ba6db4b6e391a299153af9a8211600 *man/RunPCA.Rd
89696ada8b28d6d89b5586342fac2e48 *man/SubsetSamples.Gene.Rd
ac68bcdf2981702a817ad6f20367abd4 *man/SubsetSamples.PSI.Rd
0089af644f868ed0eff6c614695d5629 *man/SubsetSamples.Rd
4024f4d18e5cdeadb5cd38a40f64e094 *man/TransformExpValues.Rd
d18d908e45697d2337098fc0c611df52 *vignettes/MARVEL.Rmd
