Files in DeLorean
Estimates Pseudotimes for Single Cell Expression Data

inst
inst/scripts
inst/scripts/McDavid-fns.R inst/scripts/Windram-DeLorean.Rmd inst/scripts/complexity.Rmd inst/scripts/test-smooth-tau.Rmd inst/scripts/Trapnell-2014.md inst/scripts/McDavid-Oscope.Rmd inst/scripts/shared.R
inst/scripts/DeLorean.bib
inst/scripts/fetch-Windram.Rmd inst/scripts/DeLorean-Trapnell.Rmd
inst/scripts/Windram-tau-posterior.eps
inst/scripts/Windram-Monocle-compare.eps
inst/scripts/parse-Kouno.Rmd inst/scripts/Shalek-DeLorean.Rmd inst/scripts/Tang-DeLorean.Rmd
inst/scripts/DeLorean-intro.Rnw
inst/scripts/fetch-Shalek-2014.Rmd inst/scripts/DeLorean-model.Rmd inst/scripts/config.R
inst/scripts/Windram-pseudotime-vs-obfuscated.eps
inst/scripts/DeLorean-inference.Rmd inst/scripts/Tang-parse.Rmd inst/scripts/McDavid-Monocle.Rmd
inst/scripts/McDavid-profiles.eps
inst/scripts/Windram-make-plots.Rmd
inst/scripts/Windram-posterior-cor.eps
inst/scripts/DeLorean-Guo.Rmd inst/scripts/McDavid-DeLorean.Rmd inst/scripts/Guo-rand-proj.Rmd inst/scripts/Kouno-DeLorean.Rmd inst/scripts/Windram-Monocle.Rmd inst/scripts/Trapnell-2014.Rmd
inst/Rmd
inst/Rmd/profiles.Rmd inst/Rmd/data.Rmd
inst/Rmd/foghorn.css
inst/Rmd/cellsizes.Rmd inst/Rmd/convergence.Rmd inst/Rmd/hyper-parameters.Rmd inst/Rmd/posterior.Rmd
inst/Stan
inst/Stan/exact-sizes.stan
inst/Stan/lowrank-sizes.stan
inst/Stan/exact.stan
inst/Stan/lowrank.stan
inst/extdata
inst/extdata/Shalek-2014-Supp-Table-2.csv
inst/extdata/gb-2013-14-10-r118-s3.csv
inst/extdata/Shalek-2014-Supp-Table-3.csv
inst/doc
inst/doc/Test_vignette.Rmd inst/doc/DeLorean.Rmd
inst/doc/DeLorean.html
inst/doc/DeLorean.R inst/doc/Test_vignette.R
inst/doc/Test_vignette.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test-guo.r
NAMESPACE
NEWS.md
data
data/WindramDeLorean.rda
data/GuoDeLorean.rda
data/KounoDeLorean.rda
R
R/report.r R/cell-size.r R/plot.r R/package.r R/model.r R/ordering.r R/held-out.r R/aov.r R/gp.r R/robustness.r R/smoothness.r R/data.r
vignettes
vignettes/DeLorean.Rmd README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/analyse.noise.levels.Rd man/fit.model.sample.Rd man/cov.calc.dists.Rd man/guo.expr.Rd man/ordering.random.block.move.Rd man/profiles.plot.Rd man/gene.covariances.Rd man/tau.offsets.plot.Rd man/ordering.improve.Rd man/knit.report.Rd man/held.out.posterior.by.variation.Rd man/kouno.expr.Rd man/centralise.Rd man/expected.sample.var.Rd man/held.out.posterior.Rd man/calc.inducing.pseudotimes.Rd man/held.out.select.genes.Rd man/plot.de.lorean.Rd man/gp.predictions.df.Rd man/cmp.profiles.plot.Rd man/inducing.covariance.Rd man/cov.matern.32.Rd man/DeLorean.Rd man/find.best.tau.Rd man/ordering.block.move.Rd man/get.posterior.mean.Rd man/make.fit.valid.Rd man/is.de.lorean.Rd man/process.posterior.Rd man/pseudotimes.pair.plot.Rd man/seriation.find.orderings.Rd man/held.out.melt.Rd man/Rhat.plot.Rd man/partition.de.lorean.Rd man/filter_genes.Rd man/make.predictions.Rd man/default.num.cores.Rd man/compile.model.Rd man/plot.held.out.posterior.Rd man/estimate.cell.sizes.Rd man/ordering.maximise.Rd man/alpha.for.rug.Rd man/de.lorean.stylesheet.Rd man/gp.log.marg.like.Rd man/fit.model.Rd man/examine.convergence.Rd man/anders.huber.cell.sizes.Rd man/ordering.is.valid.Rd man/filter_cells.Rd man/init.orderings.vs.pseudotimes.plot.Rd man/plot.add.mean.and.variance.Rd man/roughness.of.permutations.Rd man/estimate.hyper.Rd man/ordering.test.score.Rd man/expr.data.plot.Rd man/filter.cells.Rd man/avg.par.samples.Rd man/ordering.move.Rd man/aov.dl.Rd man/held.out.posterior.join.Rd man/orderings.plot.Rd man/cov.periodise.Rd man/prepare.for.stan.Rd man/de.lorean.Rd man/melt.expr.Rd man/dim.de.lorean.Rd man/test.fit.Rd man/optimise.best.sample.Rd man/pseudotimes.from.orderings.Rd man/roughness.of.sample.Rd man/held.out.posterior.filter.Rd man/find.good.ordering.Rd man/test.mh.Rd man/make.init.fn.Rd man/marg.like.plot.Rd man/fit.model.vb.Rd man/fit.dl.Rd man/windram.expr.Rd man/cov.calc.gene.Rd man/pseudotime.plot.Rd man/cov.calc.dl.dists.Rd man/ordering.metropolis.hastings.Rd man/ordering.invert.Rd man/fit.held.out.Rd man/gp.predict.Rd man/cov.calc.gene.conditioned.Rd man/report.file.Rd man/permuted.roughness.Rd man/roughnesses.plot.Rd man/analyse.variance.Rd man/print.de.lorean.Rd man/filter.genes.Rd man/find.smooth.tau.Rd man/adjust.by.cell.sizes.Rd man/mutate.profile.data.Rd man/plot.add.expr.Rd man/permute.df.Rd man/test.robustness.de.lorean.Rd man/roughness.test.Rd man/calc.roughness.Rd man/ordering.random.move.Rd man/cov.all.genes.conditioned.Rd man/gaussian.condition.Rd man/create.ordering.ll.fn.Rd
LICENSE
DeLorean documentation built on July 5, 2017, 1:04 a.m.