Package: OmicNavigator 1.19.3

Brett Engelmann

OmicNavigator: Open-Source Software for 'Omic' Data Analysis and Visualization

A tool for interactive exploration of the results from 'omics' experiments to facilitate novel discoveries from high-throughput biology. The software includes R functions for the 'bioinformatician' to deposit study metadata and the outputs from statistical analyses (e.g. differential expression, enrichment). These results are then exported to an interactive JavaScript dashboard that can be interrogated on the user's local machine or deployed online to be explored by collaborators. The dashboard includes 'sortable' tables, interactive plots including network visualization, and fine-grained filtering based on statistical significance.

Authors:Terrence Ernst [aut], John Blischak [aut], Paul Nordlund [aut], Justin Moore [aut], Joe Dalen [aut], Akshay Bhamidipati [aut], Brett Engelmann [aut, cre], Marco Curado [aut], Joe LoGrasso [aut], Elyse Geoffroy [ctb], AbbVie Inc. [cph, fnd]

OmicNavigator_1.19.3.tar.gz
OmicNavigator_1.19.3.zip(r-4.6)OmicNavigator_1.19.3.zip(r-4.5)
OmicNavigator_1.19.3.tgz(r-4.6-any)OmicNavigator_1.19.3.tgz(r-4.5-any)
OmicNavigator_1.19.3.tar.gz(r-4.6-any)
OmicNavigator_1.19.3.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OmicNavigator/json (API)
NEWS

# Install 'OmicNavigator' in R:
install.packages('OmicNavigator', repos = c('https://abbvie-external.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/abbvie-external/omicnavigator/issues

Datasets:
  • Mm.c2 - Mm.c2 from Bioconductor workflow RNAseq123
  • basal.vs.lp - Basal.vs.lp from Bioconductor workflow RNAseq123
  • basal.vs.ml - Basal.vs.ml from Bioconductor workflow RNAseq123
  • cam.BasalvsLP - Cam.BasalvsLP from Bioconductor workflow RNAseq123
  • cam.BasalvsML - Cam.BasalvsML from Bioconductor workflow RNAseq123
  • group - Group from Bioconductor workflow RNAseq123
  • lane - Lane from Bioconductor workflow RNAseq123
  • lcpm - Lcpm from Bioconductor workflow RNAseq123
  • samplenames - Samplenames from Bioconductor workflow RNAseq123

On CRAN:

Conda:

bioinformaticsgenomicsomicsopencpu

8.62 score 40 stars 53 scripts 302 downloads 73 exports 2 dependencies

Last updated from:0d35bc6134. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK209
source / vignettesOK219
linux-release-x86_64OK200
macos-devel-arm64OK154
macos-release-arm64OK139
windows-develOK213
windows-releaseOK233
windows-oldrelOK223
wasm-releaseOK116

Exports:addAnnotationsaddAssaysaddBarcodesaddEnrichmentsaddEnrichmentsLinkoutsaddFeaturesaddMappingaddMetaAssaysaddMetaFeaturesaddMetaFeaturesLinkoutsaddModelsaddObjectsaddOverlapsaddPlotsaddReportsaddResultsaddResultsLinkoutsaddSamplesaddTestscombineStudiescreateStudyexportStudygetAnnotationsgetAssaysgetBarcodeDatagetBarcodesgetEnrichmentsgetEnrichmentsAnnotationsgetEnrichmentsIntersectiongetEnrichmentsLinkoutsgetEnrichmentsModelsgetEnrichmentsNetworkgetEnrichmentsStudiesgetEnrichmentsTablegetEnrichmentsUpsetgetFaviconsgetFeaturesgetInstalledStudiesgetLinkFeaturesgetMappinggetMetaAssaysgetMetaFeaturesgetMetaFeaturesLinkoutsgetMetaFeaturesTablegetModelsgetNodeFeaturesgetObjectsgetOverlapsgetPackageVersiongetPlotsgetPlottingDatagetReportLinkgetReportsgetResultsgetResultsIntersectiongetResultsLinkoutsgetResultsModelsgetResultsStudiesgetResultsTablegetResultsTestsgetResultsUpsetgetSamplesgetStudyMetagetTestsgetUpsetColshasTermsimportStudyinstallAppinstallStudyplotStudyremoveStudystartAppvalidateStudy

Dependencies:data.tablejsonlite

OmicNavigator API

Rendered fromOmicNavigatorAPI.Rnwusingutils::Sweaveon Feb 25 2026.

Last update: 2025-12-23
Started: 2020-10-14

OmicNavigator User's Guide

Rendered fromOmicNavigatorUsersGuide.Rnwusingutils::Sweaveon Feb 25 2026.

Last update: 2025-12-16
Started: 2020-10-14

Readme and manuals

Help Manual

Help pageTopics
OmicNavigatorOmicNavigator-package OmicNavigator
Add annotationsaddAnnotations
Add assaysaddAssays
Add barcode plot metadataaddBarcodes
Add enrichment resultsaddEnrichments
Add linkouts to external resources in the enrichments tableaddEnrichmentsLinkouts
Add feature metadataaddFeatures
Add mapping objectaddMapping
Add metaAssaysaddMetaAssays
Add meta-feature metadataaddMetaFeatures
Add linkouts to external resources in the metaFeatures tableaddMetaFeaturesLinkouts
Add modelsaddModels
Add objectsaddObjects
Add overlaps between annotation gene setsaddOverlaps
Add custom plotting functionsaddPlots
Add reportsaddReports
Add inference resultsaddResults
Add linkouts to external resources in the results tableaddResultsLinkouts
Add sample metadataaddSamples
Add testsaddTests
basal.vs.lp from Bioconductor workflow RNAseq123basal.vs.lp
basal.vs.ml from Bioconductor workflow RNAseq123basal.vs.ml
cam.BasalvsLP from Bioconductor workflow RNAseq123cam.BasalvsLP
cam.BasalvsML from Bioconductor workflow RNAseq123cam.BasalvsML
Combine two or more studiescombineStudies
Create a studycreateStudy
Export a studyexportStudy
Get annotations from a studygetAnnotations
Get assays from a studygetAssays
Get data for barcode and violin plotsgetBarcodeData
Get barcodes from a studygetBarcodes
Get enrichments from a studygetEnrichments
Get the annotations for the enrichments of an installed OmicNavigator studygetEnrichmentsAnnotations
getEnrichmentsIntersectiongetEnrichmentsIntersection
Get enrichments table linkouts from a studygetEnrichmentsLinkouts
Get the models for the enrichments of an installed OmicNavigator studygetEnrichmentsModels
Get enrichments network from a studygetEnrichmentsNetwork
Get installed OmicNavigator studies that have enrichmentsgetEnrichmentsStudies
Get enrichments table from a studygetEnrichmentsTable
getEnrichmentsUpsetgetEnrichmentsUpset
Get favicon URLs for table linkoutsgetFavicons
Get features from a studygetFeatures
Get installed OmicNavigator studiesgetInstalledStudies
Get the shared features in a network linkgetLinkFeatures
Get mapping object from a studygetMapping
Get metaAssays from a studygetMetaAssays
Get metaFeatures from a studygetMetaFeatures
Get metaFeatures table linkouts from a studygetMetaFeaturesLinkouts
Get metaFeatures for a given featuregetMetaFeaturesTable
Get models from a studygetModels
Get the features in a network nodegetNodeFeatures
Get objects from a studygetObjects
Get overlaps from a studygetOverlaps
Get version of OmicNavigator packagegetPackageVersion
Get plots from a studygetPlots
Get plotting data from an OmicNavigator studygetPlottingData
Get link to reportgetReportLink
Get reports from a studygetReports
Get results from a studygetResults
getResultsIntersectiongetResultsIntersection
Get results table linkouts from a studygetResultsLinkouts
Get the models for the results of an installed OmicNavigator studygetResultsModels
Get installed OmicNavigator studies that have resultsgetResultsStudies
Get results table from a studygetResultsTable
Get the tests for the results of an installed OmicNavigator studygetResultsTests
getResultsUpsetgetResultsUpset
Get samples from a studygetSamples
Get study metadatagetStudyMeta
Get tests from a studygetTests
getUpsetColsgetUpsetCols
group from Bioconductor workflow RNAseq123group
Does an annotationID have terms available?hasTerms
Import a study packageimportStudy
Install the OmicNavigator web appinstallApp
Install a study as an R packageinstallStudy
lane from Bioconductor workflow RNAseq123lane
lcpm from Bioconductor workflow RNAseq123lcpm
Mm.c2 from Bioconductor workflow RNAseq123Mm.c2
Invoke a custom plotting functionplotStudy
Remove an installed study R packageremoveStudy
samplenames from Bioconductor workflow RNAseq123samplenames
Start app on local machinestartApp
Summarize elements of OmicNavigator studysummary.onStudy
Validate a studyvalidateStudy