All functions

IsomirDataSeq-class

Class that contains all isomiRs annotation for all samples

IsomirDataSeqFromFiles() IsomirDataSeqFromRawData()

Loads miRNA annotation from seqbuster tool or pre-processed data.

IsomirDataSeqFromMirtop()

Import mirtop output into IsomirDataSeq

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