Introduction | Installation | Data description | Algorithm description | Identifying and classifying TFs | Counting TFs per family in multiple species at once | Session information | References

Introduction | Installation | Anatomy of a GraphExperiment object | Building a GraphExperiment object | Accessing rowGraphs/colGraphs and rowData/colData (a.k.a. 'getters') | Modifying GraphExperiment objects (a.k.a. 'setters') | Subsetting GraphExperiment objects | Session information | References

Introduction | Installation | Data description | Assessing orthogroups | Protein domain-based orthogroup assessment | Reference-based orthogroup assessment | Visualizing summary statistics | Species tree | Species-specific duplications | Genes in orthogroups | Species-specific orthogroups | All in one | Orthogroup overlap | Orthogroup size per species | Session information | References

Introduction | Installation | Input data | Getting to know the example data sets | Data preparation | Classifying duplicated gene pairs and genes | The binary scheme (SD vs SSD) | The standard scheme (SSD → TD, PD, DD) | The extended scheme (SSD → TD, PD, TRD, DD) | The full scheme (SSD → TD, PD, rTRD, dTRD, DD) | Classifying genes into unique modes of duplication | Calculating substitution rates for duplicated gene pairs | Identifying and visualizing $K_s$ peaks | Classifying genes by age groups | Data visualization | Visualizing the frequency of duplicates per mode | Visualizing $K_s$ distributions | Visualizing substitution rates by species | Session information | References

Introduction | Installation | Data description | Importing data to the R session | From FASTA files to a list of AAStringSet objects | From GFF/GTF files to a GRangesList object | Data preprocessing | Synteny network inference | Phylogenomic profiling | Microsynteny-based phylogeny reconstruction | FAQ | How do I execute an external dependency that is not in my PATH? | Can I run the DIAMOND searches on the command line and import the results? | My sequence names do not match gene IDs in the annotation. What should I do? | Session information | References

Introduction | Detecting intragenome synteny | Detecting intergenome synteny | Session information | References

Introduction | Installation | Data description | Adding midparent expression values | Normalizing count data | Exploratory data analyses | Identifying differentially expressed genes between hybrids and their parents | Expression-based gene classification | Overrepresentation analysis of functional terms | Example 1: overrepresentation analyses for all expression-based classes | Example 2: overrepresentation analyses for differentially expressed genes | FAQ | Session information | References

Introduction | Installation | Data loading and preprocessing | Step-by-step data preprocessing | Automatic, one-step data preprocessing | Exploratory data analysis | Gene coexpression network analysis | Assessing module stability | Module-trait associations | Visualizing module expression profile | Enrichment analysis | Hub gene identification | Extracting subgraphs | Network visualization | Network statistics | Session information | References

Installation | Introduction and algorithm description | Data preprocessing | Consensus GRN inference | Algorithm-specific GRN inference | Gene regulatory network analysis | Hub gene identification | Network visualization | Session information | References

Installation | Introduction | Data loading and description | Consensus modules | Data preprocessing | Identification of consensus modules | Module preservation | Calculating module preservation statistics | Identifying singletons and duplicated genes | Session info | References

Introduction | Installation | Assessing genome assembly quality: statistics in a context | Obtaining assembly statistics for NCBI genomes | Comparing custom stats with NCBI stats | Visualizing summary assembly statistics | Assessing gene space completeness with BUSCO | Running BUSCO | Visualizing BUSCO summary statistics | Session information | References

Introduction | Installation | Data description | Network-based assessment of synteny identification | Session information | References

Introduction | Citation | Installation | Data description | Visualizing SNP distribution | Algorithm description | Step-by-step candidate gene mining | Step 1: finding genes close to (or in linkage disequilibrium with) SNPs | Step 2: finding coexpression modules enriched in guide genes | Step 3: finding genes with altered expression in a condition of interest | Automatic candidate gene mining | Score candidates | Session information | References

Introduction | Installation | Data description | Finding motifs | PPI V | V | Lambda | Delta | Bifan | Counting motifs and evaluating significance | Evaluting interaction similarity | Session information | References