What is omicplotR? | Introduction | Features | Installation and example | Input data | Data | Example Data | PCA Biplots | Filtering | Colouring options | Filter by metadata | Relative abundance plots | Effect plots | Contributors | Version information
Package: omicplotR 1.33.0
Daniel Giguere
omicplotR: Visual Exploration of Omic Datasets Using a Shiny App
A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata.
Authors:
omicplotR_1.33.0.tar.gz
omicplotR_1.33.0.zip(r-4.7)omicplotR_1.33.0.zip(r-4.6)omicplotR_1.33.0.zip(r-4.5)
omicplotR_1.33.0.tgz(r-4.6-any)omicplotR_1.33.0.tgz(r-4.5-any)
omicplotR_1.33.0.tar.gz(r-4.7-any)omicplotR_1.33.0.tar.gz(r-4.6-any)
omicplotR_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
omicplotR/json (API)
| # Install 'omicplotR' in R: |
| install.packages('omicplotR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:omicplotR-1.33.0(bioc 3.24)omicplotR-1.32.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaredifferentialexpressiongeneexpressionguirnaseqdnaseqmetagenomicstranscriptomicsbayesianmicrobiomevisualizationsequencingimmunooncology
Last updated from:b136580e02. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 188 | ||
| linux-devel-x86_64 | NOTE | 244 | ||
| source / vignettes | OK | 300 | ||
| linux-release-x86_64 | NOTE | 269 | ||
| macos-release-arm64 | NOTE | 128 | ||
| macos-oldrel-arm64 | NOTE | 125 | ||
| windows-devel | NOTE | 171 | ||
| windows-release | NOTE | 185 | ||
| windows-oldrel | NOTE | 169 | ||
| wasm-release | OK | 187 |
Exports:omicplotr.anosimomicplotr.clromicplotr.colouredPCAomicplotr.colvecomicplotr.filteromicplotr.getRemovedFeaturesomicplotr.getRemovedSamplesomicplotr.metadataFilteromicplotr.permanovaomicplotr.reportomicplotr.run
Dependencies:abindALDEx2base64encbayesmBHBiobaseBiocGenericsBiocParallelbslibcachemcliclustercodetoolscommonmarkcompositionscpp11crosstalkDelayedArraydeldirDEoptimRdigestdirectlabelsDTevaluatefastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvinterpIRangesjpegjquerylibjsonliteknitrlambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestNADAnlmeotelpermutepngpromisesquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRfastrlangrmarkdownrobustbaseS4ArraysS4VectorssassSeqinfoshinysnowsourcetoolsSparseArraySummarizedExperimentsurvivaltensorAtinytextruncnormveganwithrxfunxtableXVectoryamlzCompositionszigg
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'omicplotR' | omicplotR-package omicplotR |
| Internal omicplotR functions. | omicplotr.anosim omicplotr.clr omicplotr.colouredPCA omicplotr.colvec omicplotr.filter omicplotr.getRemovedFeatures omicplotr.getRemovedSamples omicplotr.metadataFilter omicplotr.permanova omicplotr.report |
| Vaginal microbiome OTU table metadata | metadata |
| Run 'omicplotR' 'Shiny' app. | omicplotr.run |
| Vaginal microbiome OTU table | otu_table |
