Package index • TimeSeriesAnalysis

All functions
`Celegans_TS_data`	RNAseq counts for Celegans and krill oil timeseries exeriment time series experiment
`DE_plots_vignettes()`	Creates differential expression results for Vignettes
`DE_using_DESeq2()`	DE with DESeq2
`DE_using_limma()`	DE using limma
`GO_dotplot_wrapper()`	Create gprofiler dotplots
`PART_heat_map()`	Create and plot PART heatmap
`PBMC_TS_data`	RNAseq counts for AID activation cocktail in PBMC time series experiment
`PBMC_pre_loaded`	Pre-computed PART and gprofiler results for the PBMC dataset
`PartRec()`	PartRec
`SS_GO_clusters()`	Find semantic similarity between clustered GOs
`TS_load_example_data()`	Add counts and sample data of examples to a TimeSeriesObject
`TimeSeries_Object-class` `TimeSeries_Object`	The TimeSeries class
`add_exp_data_tximport()`	Adds experiment data from tximport estimated reads in the form of a SummarizedExperiment
`add_experiment_data()`	Adds experiment data in the form of a SummarizedExperiment
`add_semantic_similarity_data()`	Calculate and add semantic similarity to object
`calculate_EB()`	Empirical bayesan analysis
`calculate_and_format_MDS()`	Calculate MDS matrix
`calculate_cluster_traj_data()`	Calcualte trajectory of clusters
`calculate_gene_traj_data()`	Calculate trajectory of a single gene
`calculate_mean_cluster_traj()`	Calculate mean trajectory of clusters
`celegans_pre_loaded`	Pre-computed PART and gprofiler results for the PBMC dataset
`compute_PART()`	compute PART clusters
`conditional_DE_wrapper()`	Create conditional DE results
`convert_eb_res_to_DE_results()`	Format limma DE results
`create_DEG_df()`	Create summary table for DEGs
`create_DE_data_results()`	Create and save DE results
`create_clustered_module_dataframe()`	Format clustered GO data for plotting
`create_conditional_heatmap_matrix()`	Create data for conditional heatmap
`create_example_data_for_R()`	Create a subset of count data for R examples (documentation)
`create_example_object_for_R()`	Create a TimeSeries_Object from example data
`create_raw_count_matrix()`	Prep TS matrix
`create_tables_genes_of_interest_DE()`	Creates tables and plots for genes of interest
`create_temporal_heatmap_matrix()`	Create data for temporal heatmap
`custom_gpro_dotplot()`	Create dotplot for gprofiler results
`custom_heatmap_wrapper()`	Create heatmap for differential gene expression results
`doHclust()`	doHclust
`doKmeans()`	doKmeans
`dotplot_ancestors()`	Create dotplot for ancestor query results
`exp_matrix()`	Fetches a data matrix from summarized experiments
`exp_sample_data()`	Fetches the sample data
`findPartition()`	findPartition
`findW()`	findW
`find_clusters_from_termdist()`	Cluster GO terms using Wang measurement
`find_merged_color()`	associate color to group for plotting
`find_most_variable_cluster()`	Identify cluster with the most variability
`find_relation_to_ancestors()`	Ancestor querying for GOs
`gap()`	gap
`get.threshold()`	get.threshold
`getDist()`	getDist
`getPARTlabels()`	getPARTlabels
`getReferenceW()`	getReferenceW
`gprofiler_cluster_analysis()`	Plot gprofiler results
`identify_problematic_combs()`	Identify and remove bad combs
`log_transform_l2fc_vect()`	Log transform L2FC/FC values
`maplot_alt()`	Create an MA plot
`merge_duplicate_modules()`	merge_MDS modules
`murine_TS_data`	RNAseq counts for AID activation cocktail in a murine timeseries exeriment time series experiment
`murine_pre_loaded`	Pre-computed PART and gprofiler results for the PBMC dataset
`normalize_timeSeries_with_deseq2()`	Normalize with DESeq2
`part()`	part
`part_gprofiler_vignettes()`	Gprofiler analysis for Vignettes
`part_load_results_vignettes()`	PART analysis for Vignettes
`plot_MDS()`	Create MDS plot
`plot_PCA_TS()`	Plot timeseries PCA
`plot_ancestor_clust_MDS()`	Plot nearest ancestor MDS (clustered GOs)
`plot_cluster_traj()`	Plot cluster trajectories
`plot_clustered_mds()`	plot clustered MDS
`plot_custom_DE_heatmap()`	Plots DE heatmaps
`plot_gene_traj_single_tp()`	Calculate trajectory of a single gene with no timepoints
`plot_single_gene_traj()`	Plot gene trajectory
`plot_wrapper_DE_results()`	Creates differential expression results
`prep_RNAseq_matrix()`	prep count matrix form RNAseq count files
`prep_counts_for_PART()`	Format data for PART
`prep_limma_matrix()`	Prepare data matrix from a Elist object
`prep_sample_data()`	Sample data set-up
`prep_tp_matrix()`	limma timepoint matrix
`prepare_heat_data()`	Process data for DE heatmap
`prepare_top_annotation_PART_heat()`	Create top annotation for PART heatmap
`process_microarr_dta_limma()`	Read and process microarray data using the limma package
`read_gprofiler_results()`	Read gprofiler data from results folder
`run_gprofiler_PART_clusters()`	Gprofiler analysis
`select_genes_with_l2fc()`	Select genes based on L2FC/FC
`sim()`	sim
`temporal_DE_wrapper()`	Create temporal DE results
`volcanoplot_alt()`	Create a volcano plot
`wrapper_MDS_and_MDS_clusters()`	Create MDS and nearest ancestor MDS plots
`wrapper_ancestor_curation_plots()`	Create ancestor query plots
`wrapper_cluster_trajectory()`	Plot cluster trajectory for all PART clusters
`write_example_data_to_dir()`	Prep example data in directory

Reference

All functions