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inDAGO (version 1.0.3)

A GUI for Dual and Bulk RNA-Sequencing Analysis

Description

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.

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Version

Install

install.packages('inDAGO')

Monthly Downloads

224

Version

1.0.3

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Carmine Fruggiero

Last Published

October 21st, 2025

Functions in inDAGO (1.0.3)

IndexingBulkUserInterface

Indexing bulk ui
HeatmapExp

HeatmapExp
IndexingSequentialUserInterface

Indexing sequential ui
HeatmapExpPlotly

HeatmapExpPlotly
IndexingSequentialServerLogic

Indexing sequential server logic
SummarizationServerLogic

Server function for Summarization module in Shiny application
SummarizationUserInterface

UI function for Summarization module in Shiny application
IndexingComb

Combined indexing
SequenceLengthDistributionPlot

SequenceLengthDistributionPlot
SequenceLengthDistributionPlotly

interactive SequenceLengthDistributionPlot
IndexingBulk

Bulk indexing
IndexingBulkServerLogic

Indexing bulk server logic
counting_Reads

COUNTING SEQUENCES
checkMetadata

checkMetadata
UpsetjsPlot

UpsetjsPlot
UpSetPlot

UpSetPlot
boxplotExp

boxplotExp
barplotExp

barplotExp
mappingBulkUserInterface

Mapping bulk ui
mappingBulkServerLogic

Mapping bulk server logic
EdgerDEG

EdgerDEG
QualityCheckAnalysis

QUALITY CONTROL ANALYSIS
IndexingSequentialProgressive

Indexing sequential progressive
IndexingSequentialParallel

Indexing sequential parallel
qualityControlServerLogic

Quality control server logic
WorkflowServerLogic

Server function for workflow module in Shiny application
mdsPlot

mdsPlot
WorkflowUserInterface

UI function for workflow module in Shiny application
mdsPlottly

mdsPlottly
Saturation

Saturation
mdsinfo

mdsinfo
pcainfo

pcainfo
pcaPlottly

pcaPlottly
pcaPlot

pcaPlot
volcanoPlot

volcanoPlot
qualityControlUserInterface

Quality control ui
mappingCombinedServerLogic

Mapping combined server logic
volcanoPlottly

volcanoPlottly
IndexingCombinedServerLogic

Indexing combined server logic
getDegMerged

getDegMerged
SequentialAlignment

Sequential alignment function
IndexingCombinedUserInterface

Indexing combined ui
mappingCombinedUserInterface

Mapping combined ui
Summarization

Summarization
mappingSequentialServerLogic

Mapping sequential server logic
inDAGO

inDAGO
mappingSequentialUserInterface

Mapping sequential ui
CorrPlotHeatmap

CorrPlotHeatmap
BaseAverageQualityPlot

BaseAverageQualityPlot
CorrPlotHeatmaply

CorrPlotHeatmaply
CombinedAlignment

Combined alignment for dual RNA-seq
BaseCompositionLinePlot

BaseCompositionLinePlot
BaseAverageQualityPlotly

interactive BaseAverageQualityPlot
BaseCompositionAreaChartPlot

BaseCompositionAreaChartPlot
DEGsServerLogic

Server function for DEGs module in Shiny application
BulkAlignment

Bulk alignment function
BaseQualityBoxplotPlot

BaseQualityBoxplotPlot
EDAServerLogic

Server function for EDA module in Shiny application
GCcontentDistributionPlot

GCcontentDistributionPlot
FilteringUserInterface

UI function for filtering module in Shiny application
DEGsUserInterface

UI function for DEGs module in Shiny application
FilteringServerLogic

Server function for filtering module in Shiny application
Filtering

Filtering
GCcontentDistributionPlotly

interactive GCcontentDistributionPlot
GetEdgerY

GetEdgerY
EDAUserInterface

UI function for EDA module in Shiny application