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Project

sumanth edited this page Jun 6, 2021 · 5 revisions

3 Open a Project

3.1 Open a project

The first time you work with MOG, MOG welcome dialog will not have an ”existing project” (These will appear later, based on the projects that you open). CLICK on the ”Open another project” icon, and locate a project file in your file browser. (see Download pre compiled project). Follow the prompts and the MOG main window will open. CURRENT PROJECTS. We have placed large, pre-made projects on the website for your use. These include: human, yeast, and Arabidopsis RNA-Seq data and metadata; Arabidopsis microarray data and metadata; and more (See Create Your Own Projects).

Overview

1. Introduction

2. THE BASICS: Downloading and Using MOG

3. Open a Project

4. The Main MOG GUI

5. Sort, subset, transform, analyze, and reorder the Data

6. Coexpression Analysis

7. Visualizations

8. Differential Expression Analysis

9. Dimensionality Reduction

10. Create Your Own Projects

11. Interface to R

12. Change Project Properties and MOG Properties

13. Reproducibility

1. Introduction

1.1 Introduction

1.2 How to use this guide

1.3 Citation

1.4 License

1.5 Glossary

2. The BASICS

2.1 System Requirements

2.2 Download MOG

2.3 Download a pre-compiled project

2.4 Start MetaOmGraph

2.5 Run MetaOmGraph by providing more memory(RAM)

2.6 Troubleshooting

3. Open a Project

3.1 Open a project

4. The Main MOG GUI

4.1 Save a current project

4.2 Open an existing project

5. Sort, Subset, transform, analyze, and reorder the Data

5.1 Choosing the Replicate Column

5.2 Transform Data

5.3 Feature Lists

5.4 Sample Lists

5.5 Search or Filter Sample MetaData

6. Coexpression Analysis

6.1 Correlation Between Features

6.2 Correlation Matrices

6.3 Correlation Betweeen Samples

7. Visualization

7.1 Line Charts

7.2 Line Charts with Averaged Replicates

7.3 Scatter Plot

7.4 Box Plot

7.5 Histogram

7.6 Volcano Plot

7.7 Correlation Histogram

8. Differential Expression Analysis

8.1 Differential Expression Analysis Window

8.2 Differential Expression Results Window

9. Dimensionality Reduction

9.1 Principal component analysis (PCA)

9.2 t-distributed stochastic neighbor embedding (t-SNE)

10. Create Your Own Projects

10.1 Input format

10.2 Start a new project

11. Interface to R

11.1 R script Format

12. Change Project Properties and MOG Properties

12.1 Projects Properties

12.2 MOG properties

13. Reproducibility

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