Package: mobileRNA 1.9.0

Introduction | Approach | sRNA Analysis | Information on the sRNA cluster: | Information on each sample replicate: | For mRNA Analysis | Information on the mRNA: | Installation | Installing OS Dependencies | Example Data | Example Workflow: Locating the sRNA Mobilome | Quick Start | Merging Genome Assemblies | Merging Genome Annotations | Alignment | Import Pre-Processed Data into R | Import Example Data | Identify Potential Mobile sRNA clusters | Advancing the Analysis | Core sRNA Analysis | Quality control | Plot the distribution of sRNA classes within each sample | PCA | Distance matrix heatmap | Define the consensus dicercall | Plot the consensus dicercall | Differential analysis with DESeq2 or edgeR | Save output | Differences in RNA abundance | Identify gain & loss of RNA populations | Functional analysis of gained sRNA populations | Mobile sRNA Analysis | Heatmap plots to represent mobile molecules | Functional analysis of putative mobile sRNA clusters | Add genomic attributes to sRNA clusters | Summarise sRNA cluster overlaps with genomic features | Retrieve RNA sequence from mobile sRNA clusters | Appendix | Manual sRNA Alignment Pipeline | Step 1 - De novo sRNA analysis | Step 2 - Build sRNA cluster list | Step 3 - sRNA clustering | Manual mRNA Alignment pipeline | Single-End Sequencing Reads | Pair-End Sequencing Reads | Session Information | References