57e73045e297364dacdd1e8cbb287a3a *DESCRIPTION
daf0cc97efb033777ce282411875a98b *LICENSE
02a37393f66cf1e3a3231ff1bd2e8745 *NAMESPACE
840a55c4e1eb734c52f76eabca5b0a1c *NEWS.md
6aefa93f009c6e84de44fe71c2261fb7 *R/AAUsage.R
a329cd7b31cba538459507fb4abda209 *R/CodonFreqPerGene.R
0e697b190c505c0c81cdb48323c00b6b *R/CodonUsage.R
d079911fbd7fca428a263efc0316770b *R/DifferentialExpressionAnalysis.R
fd112989b41c72a9e6ff14f2eb8e9144 *R/ExamineCodonPoolContribution.R
6b5a49e9edc8c09ddcfce871bda8d769 *R/GeneralProcessing.R
8df0174764daa80df1fef20ec8286156 *R/PermutationTest.R
0f255397d3267f63dcb6765151e03eda *R/TheoreticalTranslationEfficiency.R
2ac9429ac1a5721018276ebc909694fc *R/data.R
80c9852208123cae94c0fb3254245826 *R/sysdata.rda
e139f7b3ba33f37adb7e8e1c9c71fa46 *R/tTE_HelperFunctions_CodonFreq.R
8bfee8b0957ecdc1d2e06934e5f9b4c4 *R/tTE_HelperFunctions_CodonUsage.R
2302008e96fa26db2f56cd8c65cf7af7 *R/tTE_HelperFunctions_DEA.R
0c62bc387d1916284cac907fb0cd01ba *R/tTE_HelperFunctions_GeneralInternal.R
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67a93351b2ca903a7d0b2c825ce5ca0f *R/tTE_HelperFunctions_tTEscanRPlots.R
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df6cc46bc7fae1a55b713f3d5065b35a *R/tTEscanR-package.R
57fd806eb1f4db235cfff9879540d215 *R/tTEscanRGeneral.R
c13dd42b04ce1b8af0bc20bb1133faf9 *R/tTEscanRObject.R
770bd4aae8d9e1a3c76a7199808944e1 *README.md
21c9401b8c07f38d762ade4612fc4ffe *build/partial.rdb
f00775c7ad9f7aa17b19c450c564a77f *build/vignette.rds
947f3840f9b2c3eb2dec4f8e0fbb0b4a *data/default_tTEscanR_mRNA_data.rda
90d6caad53b4fa6d92c63629f6b26450 *data/default_tTEscanR_metadata.rda
332a70eb28d65970b6298f9e078cfe28 *data/default_tTEscanR_tRNA_data.rda
93151cd6a19cb461128768e6db61e174 *inst/doc/tTEscanR_codonfreq_module.R
57f31772ed8d53d38f49c55bad53385f *inst/doc/tTEscanR_codonfreq_module.Rmd
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77941005c4d87707d72230afa6b7807c *man/ComputeAAUsage.Rd
16c0eb151970e2e318003f7d7391a6f2 *man/ComputeAnticodonUsage.Rd
69931d8befe235e37932f9cc497b007e *man/ComputeCodonUsage.Rd
c4c18c78700e37b805065b77366372c6 *man/ComputeCorrelationBackground.Rd
85ffa31f2ebb01459ca937b605843021 *man/ComputeDEResults.Rd
42dbda67ff871aa46459695a70b0ce0f *man/ComputeExonicBackground.Rd
2ea95754813e9e341efb6f8a30022400 *man/ComputeMeanUsage.Rd
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d5843da5abc316811b48ea62bc56644a *man/ExtractCodons.Rd
ddc31bd730847be42fa2d987f9ed296a *man/FeaturesToAA.Rd
a0c3b687909dc8b25d41c91ecb385c07 *man/GetCodonFreq.Rd
3fad8002eff7851bf379523c4d474b4f *man/GetPermutationDist.Rd
29798863ba32a49fb7add2ebd5879969 *man/GroupConditions.Rd
b8b39c8bb10e210552ca9c61051f359c *man/MergeMatrices.Rd
3219b9e641459dfab579dda2633e214d *man/ObtainSignificance.Rd
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8f33d281191ca1aa70403027dee847b5 *man/PlotDEResults.Rd
cab572fca414282733e39e0aab527cf3 *man/PlotDistribution.Rd
01ca3a8f7a33d0c800791a5396171342 *man/PlotPermutation.Rd
a1fbcdfbc607520fa6994d3b3eb08ae1 *man/PlotProportion.Rd
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5c5ffe6d4ecb0f597544f3277a437b7b *man/PlotTargetComparison.Rd
2aa0f8f756640d9446a1c6ff37c6fc19 *man/RunDEAnalysis.Rd
596a7a01fba776f841689fd8b495ae30 *man/RunPipeline.Rd
6b228733a5637d3dc1fcb804f162d4fc *man/ShowPoolContribution.Rd
c35f73c1b392ca7f7c3bd6aebb6f413b *man/TransformFormat.Rd
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9f334638f8d2ade7d4d0b9f8a6f119b4 *man/computeTheoreticalTE.Rd
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928d68de8d937485405b90333e445f20 *man/tRNAGetMatrix.Rd
30a9fbfc24995a4423637e568f38321e *man/tRNASetCutoff.Rd
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e1950f981b1ec7a714f12e44f6ef64da *man/tTEscanR-package.Rd
5291f15fe9916dbd84ebd90d6e2bfd58 *tests/testthat.R
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1ecf788faa43cbc6164aa094481179e8 *tests/testthat/test_PoolContribution.R
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8dc85a742c38e0a6ffe0436bd72626c5 *tests/testthat/test_Translations.R
895625990b66f9667f75137ca86a118e *tests/testthat/test_tTEscanRHelperFunctions.R
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580d2734d3d0c106957a98e2a9b70d1e *tests/testthat/test_tTEscanRplots.R
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c8f0f276dd59fc58e82064af64424b72 *vignettes/wide_format.png
