Reference

All functions
Check_CountTable_Format()	Check the Input Count Table Format
cal_p()	Calculate the significance of the dynamic signal for a single gene's single time expression. Compared to baseline NB confidence interval.
cal_time_p_single_gene()	Calculate the significance of the dynamic signal for a single gene's over alll the time points.
combine_p_single_gene()	Combine multiple p-value using Fisher's p-value combination method.
curveFitting.new()	CurveFitting function
draw_CurveComp()	Draw DDEGs from one biological pathway from two master.list objects and also show LOESS curve fitting for both experimental groups
draw_CurveComp_Perm()	Draw DDEGs from one biological pathway from two master.list objects and also show LOESS curve fitting for both experimental groups, and perform permutation test
draw_GOHeatmap()	Draw GOHeatmap containing Terms from TimeHeatmap and included Genes
draw_GeneTraj()	Draw gene(s) trajectory with observed data and fitted data
draw_TimeHeatmap_GO()	Draw TimeHeatmap Using Gene Ontology (GO) Enrichment
draw_TimeHeatmap_enrichR()	Draw TimeHeatmap Using enrichR
draw_TimeHeatmap_selGO()	Subset TimeHeatmap by providing a manually selected non-redundant GO terms
draw_TrajClusterGrid()	Draw Grouped DDEGs Trajectories in Grid Plot
draw_TrajClusterPie()	Draw Grouped DDEGs Main-type and Sub-type Composition in Hierarchical Pie Chart
fit_single_gene_const()	Fit the baseline count data into a constant negative binomial model.
fit_single_gene_spline()	Fit the non-baseline count data into a smoothed ANOVA model.
get_GeneEnsembl2Symbol()	ID convention (from ENSEMBL to SYMBOL)
get_Symbol2GeneEnsembl()	ID convention (from SYMBOL to ENSEMBL)
get_rep_array()	Get the replicate array from count table
get_time_array()	Get the time array from count table
permutation.new()	Permutation test
preprocess_TrendCatcher()	Preprocessing for TrendCatcher
run_TrendCatcher()	Run TrendCatcher Main Algorithm
transform_single_gene_df()	Convert a single gene's count row number into data frame with two columns.