Analyze isomiRs and miRNAs from small RNA-seq

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Documentation for package ‘isomiRs’ version 1.16.2

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isomiRs-package isomiRs
counts Accessors for the count matrix of a IsomirDataSeq object.
counts-method Accessors for the count matrix of a IsomirDataSeq object.
counts.IsomirDataSeq Accessors for the count matrix of a IsomirDataSeq object.
counts<--method Accessors for the count matrix of a IsomirDataSeq object.
dat286.long Data frame containing mirna from Argyropoulos's paper
design Accessors for the 'design' slot of a IsomirDataSeq object.
design-method Accessors for the 'design' slot of a IsomirDataSeq object.
design<--method 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
IsomirDataSeq Class that contains all isomiRs annotation for all samples
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.
isomiRs 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 Method to select specific miRNAs from an IsomirDataSeq object.
isoSelect-method Method to select specific miRNAs from an IsomirDataSeq object.
isoSelect.IsomirDataSeq Method to select specific miRNAs from an IsomirDataSeq object.
isoTop Heatmap of the top expressed isomiRs
ma_ex Data frame containing gene-mirna relationship
mirData Example of IsomirDataSeq with human brain miRNA counts data
mirna2targetscan Find targets in targetscan database
mirna_ex_rse Data frame containing mirna expression data
mirTritation Data frame containing mirna from Argyropoulos's paper
updateIsomirDataSeq Update IsomirDataSeq object from version < 1.7