In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

knitr::opts_chunk$set(warning = FALSE)

Introduction

singleCellTK offers a convenient way to normalize data for downstream analysis using a number of methods available through the toolkit. The integrated normalization methods and other transformation options can be used through both R console and interactive shiny application. Normalization methods available with the toolkit include "LogNormalize", "CLR", "RC" & "SCTransform" from Seurat [@Butler2018][@Stuart2019][@Satija2017][@Hao2021] package and "logNormCounts" or "CPM" from Scater [@McCarthy2017] package. Additional transformation options are available for users including 'log' & 'log1p', trimming of data assays and Z-Score scaling.

To view detailed instructions on how to use these methods, please select 'Interactive Analysis' for using normalization in shiny application or 'Console Analysis' for using these methods on R console from the tabs below:

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## Workflow Guide

````{=html}
<div class="tab">
  <button class="tablinks" onclick="openTab(event, 'interactive')" id="ia-button">Interactive Analysis</button>
  <button class="tablinks" onclick="openTab(event, 'console')" id="console-button">Console Analysis</button>
</div>

<div id="interactive" class="tabcontent">

Normalization tab can be opened up by clicking on the Normalization & Batch Correction from the top menu and further selecting the Normalization sub-tab in the subsequent window as shown below.

Normalization tab is divided up into 4 sections as shown in the screenshot below:

The section a lets you choose a normalization method, whereas the section b allows for various options to be modified and selected for a particular normalization method selected from section a. The section c displays the overall methods/options selected for this instance of normalization process. The section d displays the output data type once the normalization is run. This output data type represents the nature of the data that will be output based on the selected options. For example, output data type maybe transformed if transformation options are selected including normalization methods, or maybe scaled if the scale option is selected. The section c and d update automatically based on normalization method and options selected by the user.

1. Select a normalization method or select Custom Normalization to manually select the options for normalization including transformation, trimming & scaling.

2a. Options when a normalization method from a particular package is selected:
i. Select the assay from the data to normalize.
ii. Set scaling factor for this particular method. These options may vary between different normalization methods. See method specific documentation for more information.
iii. Specify the name of the output data assay.
iv. Select if data should be scaled after running the normalization method.
v. Select if data should be trimmed between two values running the normalization method.
vi & vii. If trim data option is selected, specify the upper and lower trim values. The output data is then trimmed between these two values (inclusive).
viii: The user-interface displays the selected options or methods based on the user selected normalization method.
ix. The output data type based on the selected user options is displayed.
x. Click the button to run the normalization process.

2b. Options when a custom normalization is selected:
i. Select the input data assay to use as an input with selected normalization/transformation options.
ii. Specify the name of the put data assay.
iii. Select if data should be normalized (multiple normalization methods will display once this option is selected).
iv. Select if a pseudo value should be added to the data.
v. Select if the data should be scaled.
vi. Select if the data should be trimmed between two values.
vii. The user-interface displays the selected options or methods based on the user selected normalization method.
viii. The output data type based on the selected user options is displayed.
ix. Click the button to run the normalization process.

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