Estimates Pseudotimes for Single Cell Expression Data

adjust.by.cell.sizes | Adjust the expression by the estimated cell sizes. |

alpha.for.rug | Calculate a suitable value for a rug plot given the number of... |

analyse.noise.levels | Analyse noise levels and assess which genes have the greatest... |

analyse.variance | Analyse variance of expression between and within capture... |

anders.huber.cell.sizes | Estimate the cell sizes according to Anders & Huber... |

aov.dl | Perform an analysis of variance to select genes for the... |

avg.par.samples | Average across a parameters samples. |

calc.inducing.pseudotimes | Calculate inducing pseudotimes for sparse approximation |

calc.roughness | Calculate the roughness of the vector. The roughness is the... |

centralise | Centralises a periodic position into [period/2, period) by... |

cmp.profiles.plot | Plot a comparison of the profiles from several de.lorean... |

cov.all.genes.conditioned | Calculate covariances for all genes when conditioned on data... |

cov.calc.dists | Calculate distances between vectors of time points |

cov.calc.dl.dists | Calculate distances over estimated pseudotimes and test... |

cov.calc.gene | Calculate covariance structure for gene over pseudotimes and... |

cov.calc.gene.conditioned | Calculate covariance for gene over test inputs when... |

cov.matern.32 | Matern 3/2 covariance function |

cov.periodise | Makes a distance periodic |

create.ordering.ll.fn | Calculate the covariance structure of evenly spread tau and... |

default.num.cores | Default number of cores to use. |

de.lorean | Initialise DeLorean object |

DeLorean-package | The 'DeLorean' package. |

de.lorean.stylesheet | The filename of the R markdown stylesheet |

dim.de.lorean | Dimensions of DeLorean object |

estimate.cell.sizes | Estimate the cell sizes. We only consider genes that are... |

estimate.hyper | Estimate hyperparameters for model using empirical Bayes. |

examine.convergence | Analyse the samples and gather the convergence statistics.... |

expected.sample.var | The expected within sample variance of a Gaussian with the... |

expr.data.plot | Plot the expression data by the capture points |

filter_cells | Filter cells |

filter_genes | Filter genes |

find.best.tau | Find best tau to initialise chains with by sampling tau from... |

find.good.ordering | Run a find good ordering method and append results to... |

find.smooth.tau | Find best order of the samples assuming some smooth GP prior... |

fit.dl | Perform all the steps necessary to fit the model: 1. prepare... |

fit.held.out | Fit held out genes |

fit.model | Fit the model using specified method (sampling or variational... |

fit.model.sample | Fit the model using Stan sampler |

fit.model.vb | Fit the model using Stan variational Bayes |

gaussian.condition | Condition a Gaussian on another. See Eqn. A.6 on page 200 of... |

gene.covariances | Calculate the covariance structure of the tau |

get_model | Get the Stan model for a DeLorean object. |

get.posterior.mean | Get posterior mean of samples |

gp.log.marg.like | The log marginal likelihood. See "2.3 Varying the... |

gp.predict | Predictive mean, variance and log marginal likelihood of a... |

gp.predictions.df | Convert the output of gp.predict() into a data.frame. |

guo.expr | Single cell expression data and meta data from Guo et al.... |

held.out.melt | Melt held out genes |

held.out.posterior | Calculate posterior covariance and estimate parameters for... |

held.out.posterior.by.variation | Order the genes by the variation of their posterior mean |

held.out.posterior.filter | Filter the genes |

held.out.posterior.join | Join with another data frame. Useful for adding gene names... |

held.out.select.genes | Select held out genes by those with highest variance |

inducing.covariance | Calculate the covariance structure of the inducing points |

init.orderings.vs.pseudotimes.plot | Plot the orderings for initialisation against the estimated... |

is.de.lorean | Is a DeLorean object? |

knit.report | Knit a report, the file inst/Rmd/<report.name>.Rmd must exist... |

kouno.expr | Kouno et al. investigated the transcriptional network... |

make.fit.valid | Make a fit valid by running one iteration of the sampler. |

make.init.fn | Returns a function that constructs parameter settings with... |

make.predictions | Make predictions |

marg.like.plot | Plot posterior for marginal log likelihoods of individual... |

melt.expr | Melt an expression matrix. |

mutate.profile.data | Mutate the profile data into shape compatible with GP plot... |

optimise.best.sample | Optimise the best sample and update the best.sample index. |

ordering.block.move | Move a block in an ordering and shift the other items. |

ordering.improve | Improve the ordering in the sense that some function is... |

ordering.invert | Invert the ordering |

ordering.is.valid | Check that it is a valid ordering |

ordering.maximise | Find a good ordering in the sense that some function is... |

ordering.metropolis.hastings | Metropolis-Hastings on orderings. |

ordering.move | Move one item in an ordering and shift the other items. |

ordering.random.block.move | Randomly move a block in an ordering to another location |

ordering.random.move | Randomly move one item in an ordering to another location |

orderings.plot | Plot likelihoods of orderings against elapsed times taken to... |

ordering.test.score | Test ordering score: sum every time consecutive items are in... |

partition.de.lorean | Partition de.lorean object by cells |

permute.df | Permute a data frame, x. If group.col is given it should name... |

permuted.roughness | Permute cells and test roughness of expression. |

plot.add.expr | Add expression data to a plot |

plot.add.mean.and.variance | Add posterior representation to a plot. |

plot.de.lorean | Various DeLorean object plots |

plot.held.out.posterior | Plot the posterior of held out genes |

prepare.for.stan | Prepare for Stan |

print.de.lorean | Print details of DeLorean object |

process.posterior | Process the posterior, that is extract and reformat the... |

profiles.plot | Plot best sample predicted expression. |

pseudotime.plot | Plot pseudotime (tau) against observed capture time. |

pseudotimes.from.orderings | Convert best orderings into initialisations |

pseudotimes.pair.plot | Plot two sets of pseudotimes against each other. |

report.file | The filename of the R markdown report. |

Rhat.plot | Plot the Rhat convergence statistics. 'examine.convergence'... |

roughnesses.plot | Plot results of roughness test |

roughness.of.permutations | Apply permutation based roughness test to held out genes |

roughness.of.sample | Calculate the roughness of the held out genes given the... |

roughness.test | Calculate roughnesses under fit samples and also under random... |

seriation.find.orderings | Use seriation package to find good orderings |

tau.offsets.plot | Plot the tau offsets, that is how much the pseudotimes (tau)... |

test.fit | Test fit for log normal and gamma |

test.mh | Test ordering Metropolis-Hastings sampler. |

test.robustness.de.lorean | Test robustness of pseudotime estimation on subsets of... |

windram.expr | Windram et al. investigated the defense response in... |

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