# Analyze isomiRs and miRNAs from small RNA-seq

## Documentation for package ‘isomiRs’ version 1.22.0

- 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
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