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inDAGO (version 1.0.0)

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')

Version

1.0.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Carmine Fruggiero

Last Published

July 5th, 2025

Functions in inDAGO (1.0.0)

GCcontentDistributionPlotly

interactive GCcontentDistributionPlot
QualityCheckAnalysis

QUALITY CONTROL ANALYSIS
BaseAverageQualityPlotly

interactive BaseAverageQualityPlot
CorrPlotHeatmap

CorrPlotHeatmap
IndexingBulk

Bulk indexing
DEGsUserInterface

UI function for DEGs module in Shiny application
SummarizationUserInterface

UI function for Summarization module in Shiny application
SummarizationServerLogic

Server function for Summarization module in Shiny application
mappingCombinedServerLogic

Mapping combined server logic
IndexingBulkServerLogic

Indexing bulk server logic
EDAUserInterface

UI function for EDA module in Shiny application
mdsinfo

mdsinfo
Saturation

Saturation
UpSetPlot

UpSetPlot
UpsetjsPlot

UpsetjsPlot
pcaPlot

pcaPlot
WorkflowUserInterface

UI function for workflow module in Shiny application
EDAServerLogic

Server function for EDA module in Shiny application
WorkflowServerLogic

Server function for workflow module in Shiny application
GCcontentDistributionPlot

GCcontentDistributionPlot
IndexingBulkUserInterface

Indexing bulk ui
HeatmapExp

HeatmapExp
IndexingComb

Combined indexing
barplotExp

barplotExp
mappingCombinedUserInterface

Mapping combined ui
EdgerDEG

EdgerDEG
IndexingSequentialParallel

Indexing sequential parallel
IndexingSequentialProgressive

Indexing sequential progressive
SequenceLengthDistributionPlot

SequenceLengthDistributionPlot
checkMetadata

checkMetadata
SequenceLengthDistributionPlotly

interactive SequenceLengthDistributionPlot
IndexingSequentialUserInterface

Indexing sequential ui
inDAGO

inDAGO
IndexingSequentialServerLogic

Indexing sequential server logic
getDegMerged

getDegMerged
qualityControlServerLogic

Quality control server logic
boxplotExp

boxplotExp
qualityControlUserInterface

Quality control ui
mappingSequentialServerLogic

Mapping sequential server logic
mappingSequentialUserInterface

Mapping sequential ui
pcaPlottly

pcaPlottly
HeatmapExpPlotly

HeatmapExpPlotly
mappingBulkServerLogic

Mapping bulk server logic
counting_Reads

COUNTING SEQUENCES
SequentialAlignment

Sequential alignment function
pcainfo

pcainfo
mappingBulkUserInterface

Mapping bulk ui
mdsPlottly

mdsPlottly
mdsPlot

mdsPlot
Summarization

Summarization
volcanoPlottly

volcanoPlottly
volcanoPlot

volcanoPlot
BaseCompositionLinePlot

BaseCompositionLinePlot
BaseCompositionAreaChartPlot

BaseCompositionAreaChartPlot
DEGsServerLogic

Server function for DEGs module in Shiny application
BulkAlignment

Bulk alignment function
CombinedAlignment

Title
BaseQualityBoxplotPlot

BaseQualityBoxplotPlot
BaseAverageQualityPlot

BaseAverageQualityPlot
CorrPlotHeatmaply

CorrPlotHeatmaply
GetEdgerY

GetEdgerY
FilteringServerLogic

Server function for filtering module in Shiny application
Filtering

Filtering
FilteringUserInterface

UI function for filtering module in Shiny application
IndexingCombinedServerLogic

Indexing combined server logic
IndexingCombinedUserInterface

Indexing combined ui