pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Version 2.2.0

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

AuthorFederico Marini [aut, cre]
Bioconductor views DimensionReduction GUI PrincipalComponent QualityControl RNASeq ReportWriting Visualization
Date of publicationNone
MaintainerFederico Marini <marinif@uni-mainz.de>
LicenseMIT + file LICENSE
Version2.2.0
URL https://github.com/federicomarini/pcaExplorer
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pcaExplorer")

Getting started

README.md
pcaExplorer User Guide

Popular man pages

distro_expr: Plot distribution of expression values
geneprofiler: Extract and plot the expression profile of genes
genespca: Principal components analysis on the genes
get_annotation: Get an annotation data frame from biomaRt
hi_loadings: Extract genes with highest loadings
pcaExplorer: pcaExplorer: analyzing time-lapse microscopy imaging, from...
topGOtable: Extract functional terms enriched in the DE genes, based on...
See all...

All man pages Function index File listing

Man pages

correlatePCs: Principal components (cor)relation with experimental...
distro_expr: Plot distribution of expression values
geneprofiler: Extract and plot the expression profile of genes
genespca: Principal components analysis on the genes
get_annotation: Get an annotation data frame from biomaRt
get_annotation_orgdb: Get an annotation data frame from org db packages
hi_loadings: Extract genes with highest loadings
limmaquickpca2go: Functional interpretation of the principal components, based...
makeExampleDESeqDataSet_multifac: Make a simulated DESeqDataSet for two or more experimental...
pair_corr: Pairwise scatter and correlation plot of counts
pca2go: Functional interpretation of the principal components
pcaExplorer: pcaExplorer: analyzing time-lapse microscopy imaging, from...
pcaplot: Sample PCA plot for transformed data
pcaplot3d: Sample PCA plot for transformed data
pcascree: Scree plot of the PCA on the samples
plotPCcorrs: Plot significance of (cor)relations of covariates VS...
topGOtable: Extract functional terms enriched in the DE genes, based on...

Functions

correlatePCs Man page Source code
distro_expr Man page Source code
footer Source code
geneprofiler Man page Source code
genespca Man page Source code
get_annotation Man page Source code
get_annotation_orgdb Man page Source code
hi_loadings Man page Source code
limmaquickpca2go Man page Source code
makeExampleDESeqDataSet_multifac Man page Source code
pair_corr Man page Source code
pca2go Man page Source code
pcaExplorer Man page Man page Source code
pcaExplorer-package Man page
pcaplot Man page Source code
pcaplot3d Man page Source code
pcascree Man page Source code
plotPCcorrs Man page Source code
rankedGeneLoadings Source code
topGOtable Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/correlatePCs.R
R/distro_expr.R
R/genespca.R
R/get_annotation.R
R/hi_loadings.R
R/makeds.R
R/pair_corr.R
R/pca2go.R
R/pcaExplorer-pkg.R
R/pcaExplorer.R
R/pcaplot.R
R/profile_explore.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/pcaExplorer.R
inst/doc/pcaExplorer.Rmd
inst/doc/pcaExplorer.html
inst/extdata
inst/extdata/about.md
inst/extdata/instructions.md
inst/extdata/reportTemplate.Rmd
man
man/correlatePCs.Rd
man/distro_expr.Rd
man/geneprofiler.Rd
man/genespca.Rd
man/get_annotation.Rd
man/get_annotation_orgdb.Rd
man/hi_loadings.Rd
man/limmaquickpca2go.Rd
man/makeExampleDESeqDataSet_multifac.Rd
man/pair_corr.Rd
man/pca2go.Rd
man/pcaExplorer.Rd
man/pcaplot.Rd
man/pcaplot3d.Rd
man/pcascree.Rd
man/plotPCcorrs.Rd
man/topGOtable.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_correlatePCs.R
tests/testthat/test_hiloadings.R
tests/testthat/test_makeDS.R
tests/testthat/test_pca2go.R
tests/testthat/test_pcagenes.R
tests/testthat/test_pcasamples.R
tests/testthat/test_shiny.R
vignettes
vignettes/newsnap_01_upload.png
vignettes/newsnap_02_instructions.png
vignettes/newsnap_03_countstable.png
vignettes/newsnap_04_overview.png
vignettes/newsnap_05_samples.png
vignettes/newsnap_06_genes.png
vignettes/newsnap_07_finder.png
vignettes/newsnap_08_pca2go.png
vignettes/newsnap_09_multifac.png
vignettes/newsnap_10_editor.png
vignettes/newsnap_11_about.png
vignettes/pcaExplorer.Rmd
pcaExplorer documentation built on May 20, 2017, 10:13 p.m.

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