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

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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.

Author
Federico Marini [aut, cre]
Date of publication
None
Maintainer
Federico Marini <marinif@uni-mainz.de>
License
MIT + file LICENSE
Version
2.0.0
URLs

View on Bioconductor

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...

Files in this package

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