As a beginner, how to use python to analyze RNA-seq data?

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Hosein Ehsanmanesh

Hi, dear Mei.

I asked your question from ChatGPT, and the answer was:

Yes, Python is a great language for analyzing RNA-seq data. Here are some resources you can use to get started:

"RNA-seq Data Analysis: A Practical Approach" by Eija Korpelainen and Kimmo Mattila. This book provides a comprehensive introduction to RNA-seq data analysis with Python. It covers everything from pre-processing and quality control to differential gene expression analysis and functional annotation.

"Bioinformatics with Python Cookbook" by Tiago Antao. This cookbook contains a collection of recipes for analyzing biological data using Python. It includes several chapters on RNA-seq data analysis, including read mapping, differential expression analysis, and gene set enrichment analysis.

"RNA-seq analysis in Python" by Rob Patro. This tutorial provides a step-by-step guide to RNA-seq data analysis using Python. It covers topics such as read alignment, transcript quantification, and differential gene expression analysis.

"Python for Data Analysis" by Wes McKinney. Although this book is not specific to RNA-seq data analysis, it provides a solid foundation for working with data in Python. It covers topics such as data cleaning, visualization, and statistical analysis.

"RNA-seqlopedia" by the University of Toronto. This website provides a collection of tutorials and resources for RNA-seq data analysis. It includes several tutorials on using Python for RNA-seq data analysis, as well as links to other useful resources.

Moreover, to get a code, you can search on the GitHub platform (or https://paperswithcode.com/), which contains Python codes in different fields, especially analyzing RNA-seq data. you can search in the CodeOcean platform which has many codes in Python and other languages.

Mei Bao

thank you for your reply.谢谢你的答复。@Hosein Ehsanmanesh

Fezan Muhammad Ali

Yes Data Camp is good Option for Data Visualization, also you can YouTube and just with some basics of python like operator, conditional statements and python libraries like numPy, matplotlib.pyplot and pandas you can use. if not contact me I would like to help you in generating you desired visualization. [email protected]