MyRepo: General Sequencing Data Analysis and Biological Experiment Methods

This repository contains materials and notes related to sequencing data analysis and biological experiment protocols. Explore the resources below for detailed information on methods and workflows.

• To download and print the .md files

#example
pandoc  --pdf-engine=xelatex -V mainfont="Arial" file.md -o file.pdf 

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Sequencing Data Analysis Materials

Online Training and Workshops

• EMBL-EBI Online Training Courses - Comprehensive list of courses
• 3rd International Workshop on the Epigenetics of Osteoarthritis - OA Related

The important book I bought for learning Bioinformatics

• cell-line-to-command-line
• practical computing for biologists it covers regular expression, Unix commands and some python stuffs that directly related to biology

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Statistical Analysis

1. Statistical Models
2. Statistical Analysis for Mendelian Randomization (MR) Focus on things that do not change.
3. The best statistics books- Statistics will not change. The same statistics concepts will hold for many more years to come. For example, use the binomial distribution to model count data. btw, this is one of the best statistics books for biology: Modern Statistics for modern biology.

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Bioinformatics

• Bioinformatics Starter Pack

Basic R

• Understand Your Data in R
• The art of R programming, it covers the basics, learn to use packages like dplyr, ggplot2 will greatly reduce the complexity of your code and enhancer your productivity.

Basic Python

• Test the python on vs
• Book maybe useful for you python programming for absolute beginners.

Basic Linux Command Line (unix skills will never fade)

• Linux system has been around for almost 70 years. It is the same unix commands I use every day. Read this book for free
• GitHub Setup and Workflow
• Commonly used command line in HPC
• Van Andel Institute bioinfo workshop 2024-HPC
• Van Andel Institute bioinfo workshop 2024-Intro_to_Linux_for_HPC and my note

Several resources to read before any project:

• 1. A Quick Guide to Organizing Computational Biology Projects
• 2. Designing project by Vince Buffalo Vince Buffalo has a book which highly recommend: Bioinformatics data skills.
• 3. Best Practices for Scientific Computing​.The take home message for me is that it is not enough for you to just run the code, get some results and then publish them.
• 4. I learned a lot from Tommy Tang, please follow his X https://x.com/tangming2005, he tweets tools and papers. -- Dealing with genomic intervals. He mentioned in the early days, he wrote his script in python doing the same thing as bedtools (published in 2010). He mentioned Dr. Ting Wang also did the same thing, writing a Perl script to do the intersection of genomic regions and found TP53 binds to TEs. See his paper https://www.pnas.org/doi/epdf/10.1073/pnas.0703637104 in 2007. The Bioconductor ecosystem and also has the GenomicRanges package which is the foundation of dealing with genomic intervals ​

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Molecular Biology protocols

1. Protocol for Osteoclast Differentiation from Mouse Bone Marrow Monocytes
2. Protocol for Isolation and Culture of Primary Articular Chondrocytes from Mouse Growth Plate
3. Protocol for Cut&Run Assay of Mapping DNA-Protein Interactions
4. Protocol for In Vitro Cell Stretching Experiments
5. Protocol for Collect bone marrow mononuclear cells
6. Protocol for Histology: Decalcification and Immunohistochemistry (IHC)

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This repository will be continuously updated with additional methods and resources.