Analyze isomiRs and miRNAs from small RNA-seq

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Documentation for package ‘isomiRs’ version 1.36.1

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

Help Pages

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
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