16e51a7616061c2d1d07ec9769b5fba4 *DESCRIPTION
b6fd7f0a7bcc252342fc5a709a052669 *LICENSE
f0b2ec906c46f688d914049ebb17fb49 *NAMESPACE
68e0137141700fc3b0ad08464299e8e7 *NEWS
f9db44f8581b072c386ade071e21e6a1 *R/AllGenerics.R
022094fb93106e0f323a87d3c1933993 *R/OUTRIDER.R
bab98f146646644d766dc6b344b60334 *R/PCAcorrections.R
613c49055f2a5f6bd3eb688c8c514d6b *R/RcppExports.R
a53862e4b6ca57a600d17a1a78f8d0bf *R/ZscoreMatrix.R
6faf9de1ca9935a80ead4441279f7ac9 *R/autoencoder.R
73f9c3eb29c705de6002db57dbfe82ac *R/class-OutriderDataSet.R
c98a57bfcc497d8b6bc5cc7a50c0e0fb *R/controlForConfounders.R
4f558e0092611dce749dcbc6ec4ddca9 *R/filterExpression.R
7e801db6b0b7d9eca6a8ed35380f8b9a *R/fitNB.R
ae4c16d851502cd34062d27cc62ff467 *R/getNSetterFuns.R
6230fb11e0cba3c462e4805b82d9dd8c *R/getNSetterFunsInternal.R
37da44582daaca283fb403ea50a73c01 *R/helperFunctions.R
454e04c42d787d79d3326ee15f437c4b *R/inputCheckerFunctions.R
81737d7bdca5e9e0b3e706ca607bdcc5 *R/lossNGradientRVersion.R
944e3505fa5a56bb15d541095eff208a *R/method-counts.R
26069db58d0cd7453cbf24de62ecd237 *R/method-estimateBestQ.R
a149ae8c9ffb81202b0876e701e0d241 *R/method-evaluation.R
2dc223003aebfbc99f9012c5a45792f1 *R/method-plot.R
0bf8df8879d81c25757045aba935afa0 *R/method-results.R
31069ea77f448182902df58f2d604755 *R/pValMatrix.R
fe18b3034c845563e20e617165386251 *R/package-OUTRIDER.R
ef269c21746ec3df739113f1c23d2780 *R/sizeFactor.R
087db72d546d8d969b2ab8ad18708e9f *R/thetaMethodOfMoments.R
7b69558f2739f2c483316de9bd289caf *R/updateD.R
f82829a4449f0f1f727dd0de104ba605 *R/updateE.R
83f95ef0553375a35bc15234144ea8a5 *R/updateTheta.R
4329ae295539c6e4f534936b4807a497 *README.md
917345c65e07d5b3be88d2982f99a87e *build/vignette.rds
fafdbe1b774821c2557e3b20a6960a33 *inst/CITATION
e9603250001738b2ea3eac83b42595e1 *inst/doc/OUTRIDER.R
5258a9c57894addc436172a953b0cc8f *inst/doc/OUTRIDER.Rnw
c6a13374c7413e7d1700b4a8574c40bc *inst/doc/OUTRIDER.pdf
db8175a757d017a7d6fe306106d018f7 *inst/extdata/GTExSkinSmall.tsv
8b3b2a5fbac27b09d485a73a3490345d *inst/extdata/KremerNBaderSmall.tsv
dbe5dd8b87ec448d9f49aff106ceca55 *inst/extdata/gencode.v19.genes.small.gtf.gz
56fbefce5022de435f4a75cddca310b3 *man/OUTRIDER.Rd
a6abc3d5f125a13f283158aba05631f1 *man/OutriderDataSet-class.Rd
ca12266718a9a25cead52e8aa334156a *man/aberrant.Rd
bede3d8308b161c539acc51c2a1cc493 *man/computeGeneLength.Rd
97222ee1ac9befb00a7c07d01a36383c *man/computeLatentSpace.Rd
9e5e039a579ce0d5f8d09b13438cef64 *man/computePvalues.Rd
ed7433e410dba74fcbea9406cfc17f2a *man/computeZscores.Rd
604f21915b75a36841d0f623e4e78848 *man/controlForConfounders.Rd
2ef584808420ba7fd8d127073e24aaee *man/counts.Rd
169e698ab60cb4d74978050d3e7283c3 *man/estimateBestQ.Rd
3409532268a4126a42a3595083548294 *man/filterExpression.Rd
7a0fdac04e1b4ed8389e8de67d684d33 *man/fit.Rd
0d924ebb66ecb49130be5622a7b1ad73 *man/fpkm.Rd
a29ce8463090d13121c916d7f14d964e *man/getter_setter_functions.Rd
6e451b9e84b0bc10f3caa9e0272b366f *man/makeExampleOutriderDataSet.Rd
75435620a169d14a805917d7ba199ebb *man/normalizationFactors.Rd
c2a33ad518d19bb1dcd48bc5238bdf0e *man/plotFunctions.Rd
cc5592a17a483b72096588223f8760e6 *man/results.Rd
7ee195ee7bd135ea78aae53020e225d4 *man/sampleExclusionMask.Rd
89234ae8f87c7f26c47de0f4c3c5dcf7 *man/sizeFactors.Rd
3b51f08f7bbab94d56b42d6fde821bc1 *src/Makevars
3b51f08f7bbab94d56b42d6fde821bc1 *src/Makevars.win
4f3508fd2bd05a64fdadb94257a13fc3 *src/RcppExports.cpp
661c2753151d12c18f5461bdf9fe1939 *src/loss_n_gradient_functions.cpp
1378a79abc0d98f2394fec8fdefa6b33 *tests/testthat.R
2708fe9e82b4a5afad548c7024c20295 *tests/testthat/helper_test_LRsim.R
4ff8842af0a2787be8924c62ef3ed831 *tests/testthat/helper_test_data_set.R
eaea83ac4f9b42ac79700efcb4de869b *tests/testthat/test_OUTRIDERMain.R
4c8a0ff840beb749a5f08d168493604c *tests/testthat/test_OutriderDataSet.R
4862313e9a13b97fa0124a3bd90c6a47 *tests/testthat/test_Rautoenc_fit.R
d4a650fb1aae4b2d762d58c1edd72f66 *tests/testthat/test_Rautoenc_loss.R
c9cc05c9217caf2849c6c64d879111ba *tests/testthat/test_against_old_version.R
720757b484eb9bc1b7acaeb562029307 *tests/testthat/test_estimateBestQ.R
a43df017685d39636c478c1ea3ed9a8e *tests/testthat/test_filtering.R
a00e60d05ffae9aee55e38989b9d1f33 *tests/testthat/test_generics.R
ec8f25603ead43e35a5c71a2827cd00c *tests/testthat/test_helper.R
d30a1398d0f1bfbcc7212e27463e20a4 *tests/testthat/test_methods.R
7769d75f74e8f1d1f3b747b67c0a8e78 *tests/testthat/test_plotting.R
5258a9c57894addc436172a953b0cc8f *vignettes/OUTRIDER.Rnw
046715acd1e7aa2dbe52231d706f34e3 *vignettes/autoencoder_sketch.png
ff9b026b13a4b3f5870af52dfab21e04 *vignettes/bibliography.bib
b5d02a2058220cbfe05e7ce7b2b5fa05 *vignettes/gradient.pdf
b55990517392cd904a221ef8216a9b47 *vignettes/gradient.tex
