Analysis for short time-series data

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Documentation for package ‘TimeSeriesExperiment’ version 1.5.0

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.addLagsToTimeSeries Add differences to the time-course data.
.imputeData Imputing missing samples
.TimeSeriesExperiment Time Series Experiment Class
addLags Add differences to the time-course data.
assayCollapsed Collapsed data.
assayCollapsed-method Collapsed data.
assayCollapsed<- Collapsed data.
assayCollapsed<--method Collapsed data.
assignClusterDynamic Cluster assignment using dynamic branch cutting.
assignClusterStatic Cluster assignment using static branch cutting.
clusterAssignment Cluster analysis results
clusterAssignment-method Cluster analysis results
clusterData Cluster time series data.
clusterMap Cluster analysis results
clusterMap-method Cluster analysis results
clusterTimeSeries Cluster time series features.
colData<--method Column data for 'TimeSeriesExperiment'
colDataCollapsed Collapsed data.
colDataCollapsed-method Collapsed data.
colDataCollapsed<- Collapsed data.
colDataCollapsed<--method Collapsed data.
collapseReplicates Collapse data over replicates.
colnames<--method Row and column name getters and setters for 'TimeSeriesExperiment' object.
dataToTimeSeries Data to time-series
differentialExpression Differential Expression for 'TimeSeriesExperiment'
differentialExpression-method Differential Expression for 'TimeSeriesExperiment'
dimensionReduction Dimension reduction results
dimensionReduction-method Dimension reduction results
endoderm_small Endoderm differentiation
filterFeatures Filter features
groups Group information
groups-method Group information
groups<- Group information
groups<--method Group information
makeTimeSeries Convert data to time-series
makeTimeSeriesExperimentFromExpressionSet TimeSeriesExperiment constructor from ExpressionSet
makeTimeSeriesExperimentFromSummarizedExperiment TimeSeriesExperiment constructor from SummarizedExperiment
meltMatrix Melt data matrix.
normalizeData Normalize Data
pathwayEnrichment Pathway enrichment testing.
plotEnrichment Plot enrichment results.
plotHeatmap Plot a heatmap
plotSamplePCA Plot a standard PCA
plotTimeSeries Plot selected time series.
plotTimeSeriesClusters Plot (time) series over clusters.
plotTimeSeriesPCA Overlay (time) series over PCA grid
replicates Replicate information
replicates-method Replicate information
replicates<- Replicate information
replicates<--method Replicate information
rowData<--method Row data for 'TimeSeriesExperiment'
rownames<--method Row and column name getters and setters for 'TimeSeriesExperiment' object.
runPCA Run PCA scores.
show-method show method for 'TimeSeriesExperiment'
timepointDE Differential timepoint expression testing.
timepoints Timepoint information
timepoints-method Timepoint information
timepoints<- Timepoint information
timepoints<--method Timepoint information
timeSeries Time series formatted data.
timeSeries-method Time series formatted data.
timeSeries<- Time series formatted data.
timeSeries<--method Time series formatted data.
TimeSeriesExperiment Time Series Experiment Class
TimeSeriesExperiment-class Time Series Experiment Class
TimeSeriesExperiment-constructor Time Series Experiment Class
trajectoryDE Differential trajectory testing.
varianceStabilization Variance stabilization.