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Hi! I'm Tommy Tang

I am a computational biologist with six years of wet lab experience and over ten years of computation experience. I will help you to learn computational skills to tame astronomical data and derive insights. Check out the resources I offer below and sign up for my newsletter! https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources

The most important data analysis skill: PCA

Hello Bioinformatics lovers, I want to teach you how to think about data analysis. Most of the data we are analyzing is a table. In R's term, it is a dataframe or a data matrix. For any data analysis, the first step I do is usually principal component analysis or PCA. I plot PCA to spot the batch effect of the data or see if there are any outliers. But, what is PCA? At a high level, PCA tries to capture the most variance of the dataset and project the high dimension data into low dimension....

11 tools to fetch GEO and other databases' metadata and data

Hello Bioinformatics lovers, Tommy here, I am still in China and will be back in the US on July 21. Today's topic is about public data. Why do you care about it? Because if you are doing bioinformatics, public data is a gold mine for you. Without spending money to do the experiment, you can instead use others' data! but there is a problem. Public data such as GEO datasets can be hard to obtain programmatically if you do not know the tools. I have you covered! 11 tools to fetch GEO and other...

12 websites to learn computation and many others!

Hello Bioinformatics lovers, Tommy here. I am visiting China this month, but I still want to share some resources for you to learn computation. When I started learning bioinformatics in the fourth year of my PhD, I was the only one on the floor. I had no one to turn to. Then... I googled a lot and found Coursera (in 2012 when Coursera was a start-up!). It opened a new world for me. 12 years later, I have collected many more websites for you to learn. Here you go! coursera...

Where to start to learn bioinformatics?

Hello Bioinformatics lovers, One of the biggest challenges for beginners is that we do not even know where to start to learn bioinformatics. It happened to me. I figured it out the hard way. Do not worry. I am going to share 10 bioinformatics courses that you can take online. http://rafalab.dfci.harvard.edu/pages/harvardx.html by Rafa Irizarry at Dana-Farber. https://github.com/quinlan-lab/applied-computational-genomics#course-lecture-slides by Aaron Quinlan, the creator of bedtools and many...

How long it takes before you feel you are competent in Bioinformatics

Hello Bioinformatics lovers, Tommy here. I had zero programming skills 12 years ago. How long it took for me to feel confident in bioinformatics? When do I feel clicked? Today's newsletter was evoked by a post from Dean Lee. I agree it is a lifelong learning process for bioinformatics or anything in life. The moment when I feel I clicked is similar to Dean: I see a figure in a paper and I can imagine what data is needed and what process needs to take to reproduce it. In addition, I feel...

How to stand out in hundreds of bioinformatics applicants

Hello Bioinformatics lovers, Tommy again! It finally feels like summer here in Boston. The problem is too much pollen! Let's talk about Bioinformatics CV today! If you apply for a Bioinformatics position, hundreds of CVs get to sent to the hiring manager. How to stand out among all of them? Below are 6 tips from my hiring experience: Include a GitHub Link: Ensure your CV has a GitHub link with relevant content like Python or R packages, data analysis projects, or replicated figures from...

Python or R for bioinformatics?

Hello Bioinformatics lovers, I wish you a blissful Saturday! If you need to pick Python or R for bioinformatics, which one should you choose? This is my story. I started learning Unix Commands 12 years ago (See an example of how powerful Unix commands can be). I then picked up Python using "Python for absolute beginners". It was a great book, however... I did my first print("hello world") and learned the syntax of the language.. It is not that practical in terms of solving practical...

5 steps to up-level your bioinformatics skills

Hello Bioinformatics lovers, It is a Memorial Day long weekend here in the US. I hope you had a great week and learned some new skills! Today, I will show you how to up-level your bioinformatics skills in 5 steps. In the end, you will see a real example step by step. Many of the bioinformatics tutorials show you how to process one sample. However, in real life, you always need to process multiple samples. How can you do it efficiently? Level 1: do it manually. Type out the commands one by one...

essential unix program every computational biologist needs and common mistakes when analyzing scRNAseq data

Hello Bioinformatics lovers, I can not believe it is almost the middle of 2024! I hope this year you have improved your computational skills. Remember, any skills need time to be good at. Essential Unix program you need Today, I am going to introduce you an essential Unix program called "screen". I am surprised that many experienced bioinformaticians do not know it. It is a program that can give you multiple windows in a terminal and keep your ssh connection persistent. If you do not...

Most neglected skill: organize your computational biology project

Hi Bioinformatics lovers, Welcome, all the new subscribers! Every Saturday you should expect to receive this short newsletter from me. Today, we will cover one important topic that is less taught: how to organize your computational biology project. If you prefer to watch videos, watch it here. I highly recommend you read this paper: A Quick Guide to Organizing Computational Biology Projects. For every project, you should have a consistent folder structure. You do not have to follow exactly...

I am a computational biologist with six years of wet lab experience and over ten years of computation experience. I will help you to learn computational skills to tame astronomical data and derive insights. Check out the resources I offer below and sign up for my newsletter! https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources