# mobileRNA: Investigate the RNA mobilome & population-scale changes

## Documentation for package ‘mobileRNA’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

mapRNA | mobileRNA pre-processing method for sRNAseq & mRNAseq (alignment, raw count or cluster analysis)
mRNA_data | mRNA_data: simulated messenger RNA data for biological replicates
plotHeatmap | Heatmap of log-transformed normalization data
plotRNAfeatures | Plots the distribution of genomic features in the genome and those that overlap with sRNA clusters
plotSampleDistance | Sample distance matrix
plotSamplePCA | PCA plot of PC1 and PC2
RNAattributes | Overlap the genomic features related to the sRNA clusters
RNAdf2se | Convert a 'mobileRNA' dataframe to a SummarizedExperiment object
RNAdicercall | Define the consensus dicercall for each sRNA cluster
RNAdifferentialAnalysis | Differential Analysis using 'DESeq2' or 'edgeR'
RNAdistribution | Plot the distribution of sRNA classes based on nucleotide length
RNAfeatures | Summarise the distribution of sRNA clusters across genomic features
RNAimport | Import and organise sRNAseq & mRNAseq data sets
RNAmergeAnnotations | Merge two genome annotation files (GFF Format)
RNAmergeGenomes | Merge two genome reference assemblies (FASTA format)
RNAmobile | Identify putative RNA molecules produced by the non-tissue sample genome
RNApopulation | Identify gained/lost RNA populations between treatment and control conditions
RNAreorder | Reorder the data frame for differential analysis, ensuring control verse treatment comparison
RNAsequences | Extract RNA sequence from sRNA clusters
RNAsubset | Subset sRNA data based on dicercall size
RNAsummary | Summarise differential analysis results
sRNA_data | sRNA_data: simulated data for biological replicates