# Analysis for short time-series data

## Documentation for package ‘TimeSeriesExperiment’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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.