## Introduction

Data once uploaded and filtered through the preceding tabs can be normalized and corrected for batch-effect. This guide particularly focuses on normalization of data for downstream analysis which can be achieved through various methods and options integrated together in a single interface. Generally, users can use one of the provided normalization methods integrated from other packages, or use transformation options to manually normalize/scale data. Additionally, these transformation options can be applied to normalized data as well depending upon the type of the transformation.

### Available Transformation Options

Option Description
Log Transform Simple log base 2 transformation
Z-Score Standard z-score scaling
trim Trim values based on an upper and lower limits (can be applied with all of the above methods)

## Workflow Guide

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.

The Normalization user-interface is divided into three parts, a) Normalization Options, b) Assay Options, and c) Available Assays.

#### a) Normalization Options

In the Normalization Options, users can select a method for normalization from Scater - CPM or one of the methods from Seurat i.e. LogNormalize, CLR (Centered Log Ratio), RC (Relative Counts) and SCTransform. Users can also set a manual Scaling Factor (numeric value multiplied by the data values) and specify the Assay Name for the new assay.

#### b) Assay Options

In addition to the normalization methods, manually implemented transformation methods can be used to perform different transformations on the data. These transformations include Log Transform, log1p and standard Z-score.

If trimming of an assay is required, ‘Trim Assay’ option can be enabled and lower/upper bound values can be set. The default value for upper and lower trim values is 10 and -10 respectively.

#### c) Available Assays

The currently available assays are listed in the ‘Available Assays’ window. Whenever a new assay is generated, the list is updated automatically.