mobileRNA: Investigate the RNA mobilome & population-scale changes

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Documentation for package ‘mobileRNA’ version 1.4.0

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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