Reference

All functions
IsomirDataSeq-class	Class that contains all isomiRs annotation for all samples
IsomirDataSeqFromFiles()	Loads miRNA annotation from seqbuster tool or pre-processed data.
IsomirDataSeqFromMirtop()	Import mirtop output into IsomirDataSeq
IsomirDataSeqFromRawData()	Loads miRNA annotation from seqbuster tool or pre-processed data.
counts.IsomirDataSeq() counts(<IsomirDataSeq>) `counts<-`(<IsomirDataSeq>,<matrix>)	Accessors for the count matrix of a IsomirDataSeq object.
dat286.long	Data frame containing mirna from Argyropoulos's paper
design(<IsomirDataSeq>) `design<-`(<IsomirDataSeq>,<formula>)	Accessors for the 'design' slot of a IsomirDataSeq object.
ego	enrichResult class
findTargets()	Find miRNAs target using mRNA/miRNA expression
gene_ex_rse	Data frame containing gene expression data
isoAnnotate()	Annotate the rawData of the IsomirDataSeq object
isoCounts()	Create count matrix with different summarizing options
isoDE()	Differential expression analysis with DESeq2
isoNetwork()	Clustering miRNAs-genes pairs in similar pattern expression
isoNorm()	Normalize count matrix
isoPLSDA()	Partial Least Squares Discriminant Analysis for IsomirDataSeq
isoPLSDAplot()	Plot components from isoPLSDA analysis (pairs plot)
isoPlot()	Plot the amount of isomiRs in different samples
isoPlotNet()	Functional miRNA / gene expression profile plot
isoPlotPosition()	Plot nucleotides changes at a given position
isoSelect.IsomirDataSeq() isoSelect(<IsomirDataSeq>)	Method to select specific miRNAs from an IsomirDataSeq object.
isoTop()	Heatmap of the top expressed isomiRs
isomiRs-package	isomiRs
ma_ex	Data frame containing gene-mirna relationship
mirData	Example of IsomirDataSeq with human brain miRNA counts data
mirTritation	Data frame containing mirna from Argyropoulos's paper
mirna2targetscan()	Find targets in targetscan database
mirna_ex_rse	Data frame containing mirna expression data
updateIsomirDataSeq()	Update IsomirDataSeq object from version < 1.7