Package: inDAGO 1.0.3

Carmine Fruggiero

inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

A 'shiny' app that supports both dual and bulk RNA-seq, with the dual RNA-seq functionality offering the flexibility to perform either a sequential approach (where reads are mapped separately to each genome) or a combined approach (where reads are aligned to a single merged genome). The user-friendly interface automates the analysis process, providing step-by-step guidance, making it easy for users to navigate between different analysis steps, and download intermediate results and publication-ready plots.

Authors:Carmine Fruggiero [aut, cre], Gaetano Aufiero [aut]

inDAGO_1.0.3.tar.gz
inDAGO_1.0.3.zip(r-4.7)inDAGO_1.0.3.zip(r-4.6)inDAGO_1.0.3.zip(r-4.5)
inDAGO_1.0.3.tgz(r-4.6-any)inDAGO_1.0.3.tgz(r-4.5-any)
inDAGO_1.0.3.tar.gz(r-4.7-any)inDAGO_1.0.3.tar.gz(r-4.6-any)
inDAGO_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
inDAGO/json (API)

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

Bug tracker:https://github.com/indagoverse/indago/issues

On CRAN:

Conda:

4.22 score 3 stars 5 scripts 177 downloads 1 exports 158 dependencies

Last updated from:3e40df7c88. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK362
source / vignettesOK282
linux-release-x86_64OK349
macos-release-arm64OK403
macos-oldrel-arm64OK342
windows-develOK328
windows-releaseOK240
windows-oldrelOK301
wasm-releaseOK198

Exports:inDAGO

Dependencies:ade4askpassassertthatbackportsbase64encBHbiganalyticsbiglmbigmemorybigmemory.sribigtabulatebitbit64bsiconsbslibcacachemcallrcheckmateclicliprclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdendextenddigestdplyrDTeggevaluatefarverfastmapfontawesomeforeachforeignFormulafsgclusgenericsggplot2ggrepelgluegridExtragtableheatmaplyhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmatrixStatsmemoisememusemgcvmimenlmennetopensslotelpaletteerpermutepheatmappillarpixmappkgconfigplotlyplyrprettyunitsprismaticprocessxprogresspromisespspurrrqapR.devicesR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrregistryrematch2reshape2rintrojsrlangrmarkdownrpartrstudioapiS7sassscalessegmentedseqinrseriationshinyshinyAceshinycssloadersshinyFilesshinyjsshinytoastrshinyWidgetssourcetoolsspspsCompsstringistringrsvglitesyssystemfontstextshapingtibbletidyrtidyselecttinytexTSPtzdbupsetjsUpSetRutf8uuidvctrsveganviridisviridisLitevroomwebshotwithrxfunxtableyaml

Readme and manuals

Help Manual

Help pageTopics
barplotExpbarplotExp
BaseAverageQualityPlotBaseAverageQualityPlot
interactive BaseAverageQualityPlotBaseAverageQualityPlotly
BaseCompositionAreaChartPlotBaseCompositionAreaChartPlot
BaseCompositionLinePlotBaseCompositionLinePlot
BaseQualityBoxplotPlotBaseQualityBoxplotPlot
boxplotExpboxplotExp
Bulk alignment functionBulkAlignment
checkMetadatacheckMetadata
Combined alignment for dual RNA-seqCombinedAlignment
CorrPlotHeatmapCorrPlotHeatmap
CorrPlotHeatmaplyCorrPlotHeatmaply
COUNTING SEQUENCEScounting_Reads
Server function for DEGs module in Shiny applicationDEGsServerLogic
UI function for DEGs module in Shiny applicationDEGsUserInterface
Server function for EDA module in Shiny applicationEDAServerLogic
UI function for EDA module in Shiny applicationEDAUserInterface
EdgerDEGEdgerDEG
FilteringFiltering
Server function for filtering module in Shiny applicationFilteringServerLogic
UI function for filtering module in Shiny applicationFilteringUserInterface
GCcontentDistributionPlotGCcontentDistributionPlot
interactive GCcontentDistributionPlotGCcontentDistributionPlotly
getDegMergedgetDegMerged
GetEdgerYGetEdgerY
HeatmapExpHeatmapExp
HeatmapExpPlotlyHeatmapExpPlotly
inDAGOinDAGO
Bulk indexingIndexingBulk
Indexing bulk server logicIndexingBulkServerLogic
Indexing bulk uiIndexingBulkUserInterface
Combined indexingIndexingComb
Indexing combined server logicIndexingCombinedServerLogic
Indexing combined uiIndexingCombinedUserInterface
Indexing sequential parallelIndexingSequentialParallel
Indexing sequential progressiveIndexingSequentialProgressive
Indexing sequential server logicIndexingSequentialServerLogic
Indexing sequential uiIndexingSequentialUserInterface
Mapping bulk server logicmappingBulkServerLogic
Mapping bulk uimappingBulkUserInterface
Mapping combined server logicmappingCombinedServerLogic
Mapping combined uimappingCombinedUserInterface
Mapping sequential server logicmappingSequentialServerLogic
Mapping sequential uimappingSequentialUserInterface
mdsinfomdsinfo
mdsPlotmdsPlot
mdsPlottlymdsPlottly
pcainfopcainfo
pcaPlotpcaPlot
pcaPlottlypcaPlottly
QUALITY CONTROL ANALYSISQualityCheckAnalysis
Quality control server logicqualityControlServerLogic
Quality control uiqualityControlUserInterface
SaturationSaturation
SequenceLengthDistributionPlotSequenceLengthDistributionPlot
interactive SequenceLengthDistributionPlotSequenceLengthDistributionPlotly
Sequential alignment functionSequentialAlignment
SummarizationSummarization
Server function for Summarization module in Shiny applicationSummarizationServerLogic
UI function for Summarization module in Shiny applicationSummarizationUserInterface
UpsetjsPlotUpsetjsPlot
UpSetPlotUpSetPlot
volcanoPlotvolcanoPlot
volcanoPlottlyvolcanoPlottly
Server function for workflow module in Shiny applicationWorkflowServerLogic
UI function for workflow module in Shiny applicationWorkflowUserInterface