isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

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Characterization of miRNAs and isomiRs, clustering and differential expression.

Author
Lorena Pantano, Georgia Escaramis
Date of publication
None
Maintainer
Lorena Pantano <lorena.pantano@gmail.com>
License
MIT + file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

counts
Accessors for the count matrix of a IsomirDataSeq object.
find_targets
Find miRNAs target using mRNA/miRNA expression
isoCounts
Create count matrix with different summarizing options
isoDE
Differential expression analysis with DESeq2
IsomirDataSeq
Class that contains all isomiRs annotation for all samples
IsomirDataSeqFromFiles
'IsomirDataSeqFromFiles' loads miRNA annotation from...
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...
isoPLSDAplot
Plot components from isoPLSDA analysis (pairs plot)
isoSelect
Method to select specific miRNAs from an IsomirDataSeq...
isoTop
Heatmap of the top expressed isomiRs
mirData
Example of IsomirDataSeq with human brain miRNA counts data

Files in this package

isomiRs/.travis.yml
isomiRs/DESCRIPTION
isomiRs/LICENSE
isomiRs/NAMESPACE
isomiRs/NEWS
isomiRs/R
isomiRs/R/AllClasses.R
isomiRs/R/AllGenerics.R
isomiRs/R/AllMethods.R
isomiRs/R/PLSDA.R
isomiRs/R/internal.R
isomiRs/R/isomiRs.R
isomiRs/R/mirData-data.R
isomiRs/R/targets.R
isomiRs/README.md
isomiRs/TODO.md
isomiRs/build
isomiRs/build/vignette.rds
isomiRs/data
isomiRs/data/datalist
isomiRs/data/isoExample.rda
isomiRs/data/mirData.rda
isomiRs/inst
isomiRs/inst/doc
isomiRs/inst/doc/isomiRs-intro.R
isomiRs/inst/doc/isomiRs-intro.Rnw
isomiRs/inst/doc/isomiRs-intro.pdf
isomiRs/inst/extra
isomiRs/inst/extra/sample1.mirna
isomiRs/inst/extra/sample2.mirna
isomiRs/inst/unitTests
isomiRs/inst/unitTests/test_singleFunctions.R
isomiRs/man
isomiRs/man/IsomirDataSeq.Rd
isomiRs/man/IsomirDataSeqFromFiles.Rd
isomiRs/man/counts.Rd
isomiRs/man/find_targets.Rd
isomiRs/man/isoCounts.Rd
isomiRs/man/isoDE.Rd
isomiRs/man/isoNetwork.Rd
isomiRs/man/isoNorm.Rd
isomiRs/man/isoPLSDA.Rd
isomiRs/man/isoPLSDAplot.Rd
isomiRs/man/isoPlot.Rd
isomiRs/man/isoPlotNet.Rd
isomiRs/man/isoPlotPosition.Rd
isomiRs/man/isoSelect.Rd
isomiRs/man/isoTop.Rd
isomiRs/man/mirData.Rd
isomiRs/tests
isomiRs/tests/runTests.R
isomiRs/vignettes
isomiRs/vignettes/isomiRs-intro.Rnw
isomiRs/vignettes/isomirs.bib