dd3ce90ff5a90c571a6a934db6fa69d4 *DESCRIPTION
a9856e7dd03808292bce60242146f23c *NAMESPACE
eed175878d7d33419d9582d2e976c0c3 *NEWS
db52cf96fb7340977d772453091c3d4c *R/AllClasses.R
cda2a9c03934bbef2eac8fe08982a7bd *R/checkObjects.R
72ba69e72f0b6c3872b4560196c417c9 *R/compcodeR-package.R
d651bfa33328a796918399422894e374 *R/generateCodeHTMLs.R
174cb3827815985421afd22035b73680 *R/generateRmdCodeDiffExp.R
730ad07421d7ec349b43ed5097f4734d *R/generateRmdCodeDiffExpPhylo.R
bb58ba73df7ef9abbc38fc8073f3ed38 *R/generateSyntheticData.R
5ae1d98fd634614243d3dba8d827ded4 *R/phylolmMethods.R
2ab1aba08c5559b34653eac88588c845 *R/runComparison.R
cd7654413589900153ec914ba4c9aaf5 *R/runComparisonShiny.R
0c9446e83470a005044a5e6921dd3f99 *R/runDiffExp.R
2cc03e438f6862f58418a91ab45fbd3f *R/show-methods.R
a574b27d19436c03a1e80899441532cd *R/simulatePhyloPoissonLogNormal.R
52204e1ab58d8dd1c57cfa203c62b1ff *README.md
9043cefcc3a2965f3768df2c943d8282 *build/vignette.rds
dedd5896dffeaf7c4a4166129dff9ff8 *inst/CITATION
2a9db4e0d58a4203a5fc0531f3a9665e *inst/doc/compcodeR.R
c1ee90ff0bf7eabb22bb78aee666c458 *inst/doc/compcodeR.Rmd
26217e048c1dc7e7403b87bacded9973 *inst/doc/compcodeR.html
6522a017a26d9bd25c881d935c6db1b2 *inst/doc/phylocompcodeR.R
0361a374c625d3edac1ead61e89d5c91 *inst/doc/phylocompcodeR.Rmd
af96f59ccb6410565504f6b77effd544 *inst/doc/phylocompcodeR.html
23e802cbd54d5511490dade08a675141 *inst/extdata/Pickrell.Cheung.Mu.Phi.Estimates.rds
42950f82241423cc8140c210a30fdd2e *inst/extdata/Stern2018.Length.Mu.Phi.Estimates.rds
d4921c6a012b3a3d6c86e7ef7483b37a *inst/extdata/Stern2018.tree
b2317fa147f7db593910b990254de1ed *man/DESeq2.createRmd.Rd
417963b2acc4f27e5b7b0559737c0559 *man/DESeq2.length.createRmd.Rd
08ec7ee921fa23d9de8d0bcd07fe5816 *man/DSS.createRmd.Rd
7ea5d5ad774845f8dfb2aa664f5046de *man/EBSeq.createRmd.Rd
f9fcbb13daa7771b1a0ac509288e4cfe *man/NBPSeq.createRmd.Rd
6b8b3d9915f89c64c3776340512fd9ef *man/NB_to_PLN.Rd
c059228d41257f04470407026c5ea923 *man/NOISeq.prenorm.createRmd.Rd
08e8234b00ef0c0a5463302dca585083 *man/TCC.createRmd.Rd
57aadd1c3ac3c72b92c69ac917ef80e5 *man/add_replicates.Rd
4b9cfa50b78a03b048f7ea4b568df71c *man/checkDataObject.Rd
c52ffaa3731fc00041dc802801017adf *man/checkParamMatrix.Rd
1ddc35b5556168b80f3ab48777779810 *man/checkParamVector.Rd
58c0be4f3f21453335b3368978b072d1 *man/checkSpecies.Rd
dc828e89ffc30ba7a6710d267fd43e15 *man/checkTableConsistency.Rd
da2cafdc2b08a5f07b9fe9793fcdf173 *man/check_compData.Rd
800b372925a6705b85593f91bd5642bc *man/check_compData_results.Rd
98bb770417e926845cc0883691db1e36 *man/check_phyloCompData.Rd
83e8d0aa05b25b1c15a2ec67ad8bd0fd *man/compData-class.Rd
fc01a25d4567dbb2b4afaed8f0492a62 *man/compData.Rd
0e2842f68b613e5f5c1afa9f79225243 *man/compcodeR-package.Rd
3a657b51e60144c12d0980317291b019 *man/computeFactorLengths.Rd
e60e8ca390626df5f36a6be04a36fd15 *man/convertListTocompData.Rd
d8b27544f98daea0686a4d831e561cb0 *man/convertListTophyloCompData.Rd
50892908cea2ca46ba954045417114da *man/convertcompDataToList.Rd
a609928dc9b7efca630b4d91eac950e5 *man/convertphyloCompDataToList.Rd
dc72d3e629f93856f6c60a7cb5980e9d *man/edgeR.GLM.createRmd.Rd
4402ee65608762e02f28af749f8d00c4 *man/edgeR.exact.createRmd.Rd
ad1a25b9c209ca9293b609a798d91e02 *man/extract_results_phylolm.Rd
ead1b57b8d211a1f785f551b80e53914 *man/generateCodeHTMLs.Rd
06fde6256650685ad6e9bd96c23f83de *man/generateLengths.Rd
feb0082d07723e2596020227013fdf4c *man/generateLengthsPhylo.Rd
8d69420744a0065d196b810dd5c31664 *man/generateSyntheticData.Rd
41c86c0d0d91589967549b82f43cd5bb *man/getNegativeBinomialDispersion.Rd
3e71c4119089870b26b1200551dbbb36 *man/getNegativeBinomialMean.Rd
aada2145e93e880b0e6702d7a32be120 *man/getNegativeBinomialParameters.Rd
f8000df63b400439abffe7e81ed8cd7b *man/getTree.Rd
af3ff0f6557ab3495c3b5b34e5fbcea3 *man/get_model_factor.Rd
b4f2f67cb12065d106cebac078dfe62f *man/get_poisson_log_normal_parameters.Rd
1ea5c445e309de2b8e437440e85c0bc7 *man/lengthNorm.limma.createRmd.Rd
4c0b2c9d94e0a697814ccfcee6e9e7fb *man/lengthNorm.sva.limma.createRmd.Rd
83aa9f4f112695d0133c26184ecd22ce *man/listcreateRmd.Rd
699da664181c10a8447c3cc2675305bc *man/logcpm.limma.createRmd.Rd
73820600aa4e7255491ddf641a54ab36 *man/nEffNaive.Rd
a55f3461cae3db99a8ab1b3442b63eaa *man/nEffRatio.Rd
7ecce28fd818448b5d6dec156560bafd *man/phyloCompData-class.Rd
050179249b3595002baeb18f4e51b225 *man/phyloCompData.Rd
d37377efe24baafe071e44dbe574f15f *man/phyloCompDataFromCompData.Rd
aff4f093344a4ff4d1ba919ac8f5c013 *man/phylolm.createRmd.Rd
bea05747bbc57833b580dc5f0edc98d0 *man/phylolm_analysis.Rd
d3a91a2ed94a4c9becf942d439fdae1e *man/runComparison.Rd
d7bfe23167bbd931c86e4b9157087c9f *man/runComparisonGUI.Rd
d2a52320194835f311a331fa7af8b35d *man/runComparisonShiny.Rd
c811bc7d0dcf893a5b566a18b5358468 *man/runDiffExp.Rd
787efd8d66b44588560ea8d09a4fcaab *man/scale_variance_process.Rd
96b4d7751395e4ea149ca5b85ee3dcff *man/show-compData-method.Rd
59f0ac76288e33b6d7baeb2d60a0c305 *man/show-phyloCompData-method.Rd
479129cb1e70a323cef213d87b696c10 *man/show_compData.Rd
43ea4910ea9c24e581dc3e99d8fb6603 *man/simulateData.Rd
e3d45fdcbddd1164494e91563be4019e *man/simulateDataPhylo.Rd
ee275d065438b222a09cd79ba62f64ea *man/simulatePhyloPoissonLogNormal.Rd
37f646d3380985cfbf50db515a86552b *man/sqrtcpm.limma.createRmd.Rd
72f9ffe041c3c6bd5170fbe6cc8684da *man/summarizeSyntheticDataSet.Rd
19d39810f7f4f3e4aebfa490a77f5df2 *man/ttest.createRmd.Rd
7a33816bfec526f0e4ccfacb2f3de4f4 *man/voom.limma.createRmd.Rd
cff9e58142105a8953ed5215db55b57d *man/voom.ttest.createRmd.Rd
cdea0bcfae55873b68fedd1c4be70c5d *man/writeNormalization.Rd
7d332d74a4423fe1a1a2a50835620be5 *tests/testthat.R
1c4cc5b71938529ea721647270f2af0d *tests/testthat/test-moments_NB_PLN.R
81e2b8ed6428c8a7f1305028062ee1b6 *tests/testthat/test-runComparison.R
4d1f64ce2f663c7b2f8cb8a4668161ec *tests/testthat/testEffectiveSampleSize.R
9c5bc43a3df2136fb412c9437abcb8fc *tests/testthat/testNBtoPLN.R
5a10df7deea1dcb00ec4cc6e650903de *tests/testthat/test_length_factors.R
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2bb81a6a882195ef26659e2d75f06fc1 *vignettes/compcodeR.bib
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