Model-based Analysis of Single Cell Transcriptomics

applyFlat | Apply a vectorized binary operation recycling over last... |

BayesGLMlike-class | Wrapper for bayesian GLM |

bootVcov1 | Bootstrap a zlmfit |

calcZ | Get Z or T statistics and P values after running... |

cData | Deprecated cell/feature data accessors/mutators |

colData-set-SingleCellAssay-DataFrame-method | Replace 'colData' |

collectResiduals | Residual hooks and collection methods |

computeEtFromCt | Compute the Et from the Ct |

convertMASTClassicToSingleCellAssay | Convert a MASTClassic SingleCellAssay |

defaultPrior | Initialize a prior to be used a prior for... |

dof | Degrees of freedom of Zero inflated model |

Drop | Drop specified dimension from an array |

ebayes | Estimate hyperparameters for hierarchical variance model for... |

expavg | Exponential average |

fData-methods | fData |

featureData-methods | Accessor for featureData 'AnnotatedDataFrame' |

filter | Filter a SingleCellAssay |

filterLowExpressedGenes | Filter low-expressing genes |

fit | fit a zero-inflated regression |

freq | Summary statistics for genes in an experiment |

FromFlatDF | Construct a SingleCellAssay (or derived subclass) from a... |

FromMatrix | Construct a SingleCellAssay from a matrix or array of... |

getConcordance | Get the concordance between two experiments |

getwellKey | Accessor for wellKey |

GLMlike-class | Wrapper for regular glm/lm |

gseaAfterBoot | Gene set analysis for hurdle model |

GSEATests-class | An S4 class for Gene Set Enrichment output |

hushWarning | Selectively muffle warnings based on output |

Hypothesis | Describe a linear model hypothesis to be tested |

impute | impute missing continuous expression for plotting |

influence.bayesglm | Influence bayesglm object |

invlogit | Inverse of logistic transformation |

LMERlike-class | Wrapper for lmer/glmer |

LMlike-class | Linear Model-like Class |

logFC | Calculate log-fold changes from hurdle model components |

logmean | Log mean |

LRT | Likelihood Ratio Tests for SingleCellAssays |

lrTest | Run a likelihood-ratio test |

lrTest-ZlmFit-character-method | Likelihood ratio test |

maits-dataset | MAITs data set, RNASeq |

MAST-package | MAST: Model-based Analysis of Single- cell Transcriptomics |

melt.SingleCellAssay | "Melt" a 'SingleCellAssay' matrix |

model.matrix | Model matrix accessor |

model.matrix-set | Replace model matrix |

myBiplot | Makes a nice BiPlot |

pbootVcov1 | Bootstrap a zlmfit |

plotlrt | Plot a likelihood ratio test object |

plotSCAConcordance | Concordance plots of filtered single vs n-cell assays |

plot.thresholdSCRNACountMatrix | Plot cutpoints and densities for thresholding |

predict.ZlmFit | Return predictions from a ZlmFit object. |

primerAverage | Average expression values for duplicated/redundant genes |

print.summaryZlmFit | Print summary of a ZlmFit |

read.fluidigm | Reads a Fluidigm Biomark (c. 2011) raw data file (or set of... |

removeResponse | Remove the left hand side (response) from a formula |

rstandard.bayesglm | rstandard for bayesglm objects. |

se.coef | Return coefficient standard errors |

show | show |

split-SingleCellAssay-character-method | Split into 'list' |

stat_ell | Plot confidence ellipse in 2D |

subset-SingleCellAssay-method | Subset a 'SingleCellAssay' by cells (columns) |

summarize | Return programmatically useful summary of a fit |

summary-GSEATests-method | Summarize gene set enrichment tests |

summary.thresholdSCRNACountMatrix | Summarize the effect of thresholding |

summary-ZlmFit-method | Summarize model features from a 'ZlmFit' object |

thresholdSCRNACountMatrix | Threshold a count matrix using an adaptive threshold. |

vbeta-dataset | Vbeta Data Set |

vbetaFA-dataset | Vbeta Data Set, FluidigmAssay |

waldTest | Run a Wald test |

waldTest-ZlmFit-matrix-method | Wald test |

xform | Make matrix of continuous expression values, orthogonal to... |

zlm | Zero-inflated regression for SingleCellAssay |

ZlmFit-class | An S4 class to hold the output of a call to zlm |

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