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