mobileRNA: Investigate the RNA mobilome & population-scale changes

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Documentation for package ‘mobileRNA’ version 1.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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