IndexingBulk

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.

Carmine Fruggiero

inDAGO

A GUI for Dual and Bulk RNA-Sequencing Analysis

Gaetano Aufiero

IndexingBulk function

<dl><dt>basename</dt>
<dd>output basename</dd>
<dt>reference</dt>
<dd>reference genome</dd>
<dt>gappedIndex</dt>
<dd>gapped structure</dd>
<dt>indexSplit</dt>
<dd>split structure</dd>
<dt>memory</dt>
<dd>handling memory</dd>
<dt>TH_subread</dt>
<dd>threshold memory usage</dd></dl>

Arguments

Bulk indexing — IndexingBulk

<dl>

<dt>basename</dt>
<dd>output basename</dd>


<dt>reference</dt>
<dd>reference genome</dd>


<dt>gappedIndex</dt>
<dd>gapped structure</dd>


<dt>indexSplit</dt>
<dd>split structure</dd>


<dt>memory</dt>
<dd>handling memory</dd>


<dt>TH_subread</dt>
<dd>threshold memory usage</dd>

</dl>

IndexingBulk: Bulk indexing

Description

Usage

Arguments