isomiRs: Analyze isomiRs and miRNAs from small RNA-seq
Version 1.4.0

Characterization of miRNAs and isomiRs, clustering and differential expression.

AuthorLorena Pantano, Georgia Escaramis
Bioconductor views Clustering DifferentialExpression RNASeq miRNA
Date of publicationNone
MaintainerLorena Pantano <lorena.pantano@gmail.com>
LicenseMIT + file LICENSE
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("isomiRs")

Getting started

README.md

Popular man pages

counts: Accessors for the count matrix of a IsomirDataSeq object.
isoDE: Differential expression analysis with DESeq2
isoNorm: Normalize count matrix
isoPlot: Plot the amount of isomiRs in different samples
isoPlotPosition: Plot nucleotides changes at a given position
isoPLSDA: Partial Least Squares Discriminant Analysis for...
mirData: Example of IsomirDataSeq with human brain miRNA counts data
See all...

All man pages Function index File listing

Man pages

counts: Accessors for the count matrix of a IsomirDataSeq object.
design: Accessors for the 'design' slot 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

Functions

IsoCountsFromMatrix Source code
IsomirDataSeq Man page Source code
IsomirDataSeq-class Man page
IsomirDataSeqFromFiles Man page Source code
R2PermutationVector Source code
R2RefinedPermutationVector Source code
apply_median Source code
change_seq Source code
clean_low_rate_changes Source code
cluster_exp Source code
collapse_mirs Source code
convert_to_new_version Source code
cor_matrix Source code
counts Man page Man page
counts,IsomirDataSeq-method Man page Man page
counts.IsomirDataSeq Man page Source code
counts<-,IsomirDataSeq,matrix-method Man page
design Man page Man page
design,IsomirDataSeq-method Man page
design.IsomirDataSeq Source code
design<-,IsomirDataSeq,formula-method Man page
filter_by_cov Source code
filter_table Source code
find_targets Man page Source code
from_pairs_to_matrix Source code
isoCounts Man page Source code
isoDE Man page Source code
isoNetwork Man page Source code
isoNorm Man page Source code
isoPLSDA Man page Source code
isoPLSDAplot Man page Source code
isoPlot Man page Source code
isoPlotNet Man page Source code
isoPlotPosition Man page Source code
isoSelect Man page
isoSelect,IsomirDataSeq-method Man page Man page
isoSelect.IsomirDataSeq Man page Source code
isoTop Man page Source code
median_by_group Source code
mirData Man page
no_na Source code
plot_profiles Source code
put_header Source code
reduce_mirna Source code
run_enricher Source code
scale Source code
somir_general_type Source code
somir_position Source code
subs_position Source code
summary_mirna Source code
viz_mirna_gene_enrichment Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/AllMethods.R
R/PLSDA.R
R/internal.R
R/isomiRs.R
R/mirData-data.R
R/targets.R
README.md
TODO.md
build
build/vignette.rds
data
data/datalist
data/isoExample.rda
data/mirData.rda
inst
inst/doc
inst/doc/isomiRs-intro.R
inst/doc/isomiRs-intro.Rnw
inst/doc/isomiRs-intro.pdf
inst/extra
inst/extra/sample1.mirna
inst/extra/sample2.mirna
inst/unitTests
inst/unitTests/test_singleFunctions.R
man
man/IsomirDataSeq.Rd
man/IsomirDataSeqFromFiles.Rd
man/counts.Rd
man/design.Rd
man/find_targets.Rd
man/isoCounts.Rd
man/isoDE.Rd
man/isoNetwork.Rd
man/isoNorm.Rd
man/isoPLSDA.Rd
man/isoPLSDAplot.Rd
man/isoPlot.Rd
man/isoPlotNet.Rd
man/isoPlotPosition.Rd
man/isoSelect.Rd
man/isoTop.Rd
man/mirData.Rd
tests
tests/runTests.R
vignettes
vignettes/isomiRs-intro.Rnw
vignettes/isomirs.bib
isomiRs documentation built on May 20, 2017, 9:13 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.