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()

Use Case #1: Functional Annotation of Genes Sharing a Common Evolutionary History | Step 1 | Enrichment Analyses

Topics | Perform Meta-Genome Retrieval | Getting Started | Retrieve Genomic Sequences | Example NCBI RefSeq: | Example NCBI Genbank: | Example ENSEMBL | Retrieval from NCBI RefSeq | Restarting a corrupted download | Un-zipping downloaded files | Retrieval from NCBI Genbank | Retrieval from ENSEMBL | Retrieve groups or subgroups of species | Example retrieval of all Gammaproteobacteria genomes from NCBI RefSeq: | Example retrieval of all Adenoviridae genomes from NCBI RefSeq: | Meta retrieval of genome assembly quality information | Metagenome project retrieval from NCBI Genbank | Retrieve Protein Sequences | Retrieval from NCBI RefSeq: | Retrieval from NCBI Genbank: | Retrieval from ENSEMBL: | Retrieve CDS Sequences | Retrieve GFF files | Retrieve GTF files | Retrieve RNA sequences | Retrieve Repeat Masker Sequences | Retrieve Individual Genomes for all Species in the Tree of Life | Genome Retrieval | Proteome Retrieval

Biological Sequence Retrieval | Topics | Getting Started with Sequence Retrieval | Example NCBI RefSeq (?is.genome.available): | Using the NCBI Taxonomy ID instead of the scientific name to screen for organism availability | Using the accession ID instead of the scientific name or taxid to screen for organism availability | A small negative example | Example NCBI Genbank (?is.genome.available): | Using is.genome.available() with ENSEMBL | Example ENSEMBL (?is.genome.available): | Example UniProt (?is.genome.available): | Listing the total number of available genomes | Retrieving kingdom, group and subgroup information | Analogous computations can be performed for groups and subgroups | Downloading Biological Sequences and Annotations | Genome Retrieval | Example NCBI RefSeq: | Use taxid id for genome retrieval | Use assembly_accession id for genome retrieval | Example NCBI Genbank: | Use taxonomy id for genome retrieval | Example ENSEMBL: | GenomeSet Retrieval | Proteome Retrieval | Example Retrieval Uniprot: | ProteomeSet Retrieval | CDS Retrieval | CDSSet Retrieval | RNA Retrieval | RNASet Retrieval | Retrieve the annotation file of a particular genome | Removing corrupt lines from downloaded GFF files | GFFSet Retrieval | Repeat Masker Retrieval | Genome Assembly Stats Retrieval | Collection Retrieval

Functional Annotation Retrieval from Ensembl Biomart | Getting Started | The old biomaRt query methodology | Extending biomaRt using the new query system of the biomartr package | Getting Started with biomartr | Retrieve marts, datasets, attributes, and filters with biomartr | Retrieve Available Marts | Retrieve Available Datasets from a Specific Mart | Retrieve Available Attributes from a Specific Dataset | Retrieve Available Filters from a Specific Dataset | Organism Specific Retrieval of Information | Construct BioMart queries with biomartr | Gene Ontology | GO Annotation Retrieval via BioMart

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

Retrieve Sequence Databases from NCBI | Getting Started | List available databases | Download NCBI databases | Example NCBI nr | Example NCBI nt | Example NCBI RefSeq | Example PDB | Example NCBI Taxonomy | Example NCBI Swissprot | Example NCBI CDD Delta