Taxonomic Information Retrieval | Retrieve Children Nodes

What is genomic phylostratigraphy? | Gene age information in TAI | The debate | Homology search bias | Alternatives to BLASTp | Open questions | Summary

Gallery of different plots available with myTAI | Bulk RNA-seq data | myTAI plots can be modified as a ggplot2 object. | Transformation and robustness checks | Statistical tests and plotting results | Average gene expression level by phylostratum | Contribution to the overall TAI by phylostratum | Contribution to the overall TAI by partial TAI (pTAI) | Phylostratum distribution | Expression heatmap | Dimension reduction | At the gene level | At the sample level | Inspecting mean-variance relationship | Individual gene expression profiles | Single cell RNA-seq data | Single-cell signature plots | Other single-cell visualizations

The motivation for transformating of RNA-seq data | Transforming RNA-seq data for myTAI | Other robustness checks | Transforming gene age information for myTAI | Conclusion

Motivation for breaking the hourglass | Break the hourglass using gaTAI

S7 BulkPhyloExpressionSet and ScPhyloExpressionSet objects | Constructing BulkPhyloExpressionSet and ScPhyloExpressionSet | Loading raw data | Mock (bulk) dataset for BulkPhyloExpressionSet | Bulk RNA-seq data without replicates | What if the dataset contains replicates? | Mock single-cell dataset for ScPhyloExpressionSet | Summary

Motivation for non-TAI approaches | Transcriptome divergence index (TDI) | Mock bulk RNA-seq dataset for TDI | Transcriptome specificity index (TSI) | Transcriptome {insert your idea} index | Summary

The motivation for statistically-informed analysis of TAI patterns | Statistical analysis of TAI patterns | Flatline test | Cullen and Frey plot | Null distribution visualisation | Reductive hourglass test and other time-course tests | Reductive hourglass test | Reverse hourglass test | Early conservation test | Late conservation test | Pairwise test | Summary

Introduction to the philentropy Package | Distance Measures | Distance and Similarity Measures | $L_p$ Minkowski Family | $L_1$ Family | Intersection Family | Inner Product Family | Squared-chord Family | Squared $L_2$ family ($X^2$ squared family) | Shannon's Entropy Family | Combinations | Information Theory

dist_one_one() | dist_one_many() | dist_many_many()

How to use distance() | Simple Example

Information Theory measures in philentropy | Shannon's Entropy H(X) | Shannon's Joint-Entropy H(X,Y) | Shannon's Conditional-Entropy H(X | Y) | Mutual Information I(X,Y) | Kullback-Leibler Divergence | Jensen-Shannon Divergence | Properties of the Jensen-Shannon Divergence: | Generalized Jensen-Shannon Divergence