Review

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. In my last blog post, I showed you how to download TCGA RNAseq count data and do PCA and make a heatmap. It is interesting to see some of the LUSC samples mix with the LUAD samples and vice versa. In this post, we will continue to use PCA to do more Exploratory data analysis (EDA).

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. In my last post, I showed you how to use PCA for bulk RNAseq data. Today, let’s see how we can use it for scATACseq data. Download the example dataset from 10x genomics https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_pbmc_5k_v1 The dataset is 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v1.0). Download the atac_pbmc_5k_v1_filtered_peak_bc_matrix.tar.gz file and unzip it.

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. what is PCA? Principal Component Analysis (PCA) is a mathematical technique used to reduce the dimensionality of large datasets while preserving the most important patterns in the data. It transforms the original high-dimensional data into a smaller set of new variables called principal components (PCs), which capture the most variation in the data.

In a biotech startup, an early data strategy is key to ensure public and private data remain useful and valuable. As AI hype reaches new heights, I want to emphasize that a data strategy must precede any AI strategy. Data is the oil of the AI engine. Unfortunately, the real-world data are usually messy and not AI-ready. Without a robust data strategy, you are building an AI system on a shaky foundation.

As 2024 wraps up, it’s the perfect time to reflect and prepare for the new year. I wrote the review for 2023 here. Goals reached ✅ I lost 12 lb in 6 weeks! ✅ Supported the clinical trial to identify bio markers for potential responders to our drug at Immunitas. Helped with indication selection for the second and third program. I moved to Astrazeneca in August. I really appreciate my experience at Immunitas and learned a lot.

Every year, I write a review for the past 12 months. Find my review for 2021. Some top wins: Anna was born in September! It is a lot of work with three kids, but they are cute! I am grateful for our CSO Thomas Tan, who has confidence in me to lead the team. We built an amazing computational biology team at Immunitas. I am so fortunate to have Matt, Tim and Michelle in the group.

It is almost the end of 2018. It is a good time to review what I have achieved during the year and look forward to a brand new 2019. I wrote a similar post for 2017 here. Some highlights of the year 2018: My son Noah Tang was born in April. He is so lovely and we love him so much. Can’t believe he is almost 9 months old.