All functions

counts.IsomirDataSeq counts counts<-

Accessors for the count matrix of a IsomirDataSeq object.

dat286.long

Data frame containing mirna from Argyropoulos's paper

design design<-

Accessors for the 'design' slot of a IsomirDataSeq object.

findTargets

Find miRNAs target using mRNA/miRNA expression

gene_ex_rse

Data frame containing gene expression data

isoCorrect

Correct miRNA expression based on prior ligation bias information

isoCounts

Create count matrix with different summarizing options

isoDE

Differential expression analysis with DESeq2

isoLQNO

Differential expression between two groups using LQNO model

Class that contains all isomiRs annotation for all samples

IsomirDataSeqFromFiles

IsomirDataSeqFromFiles loads miRNA annotation from seqbuster tool

isomiRs

isoNetwork

Clustering miRNAs-genes pairs in similar pattern expression

isoNorm

Normalize count matrix

isoPlot

Plot the amount of isomiRs in different samples

isoPlotNet

Functional miRNA / gene expression profile plot

isoPlotPosition

Plot nucleotides changes at a given position

isoPLSDA

Partial Least Squares Discriminant Analysis for IsomirDataSeq

isoPLSDAplot

Plot components from isoPLSDA analysis (pairs plot)

isoSelect.IsomirDataSeq isoSelect

Method to select specific miRNAs from an IsomirDataSeq object.

isoTop

Heatmap of the top expressed isomiRs

dLQNO pLQNO qLQNO rLQNO LQNO

LQNO distribution

ma_ex

Data frame containing gene-mirna relationship

data

Example of IsomirDataSeq with human brain miRNA counts data

mirna_ex_rse

Data frame containing mirna expression data

mirTritation

Data frame containing mirna from Argyropoulos's paper