Director of computational biology. On my way to helping 1 million people learn bioinformatics. Educator, Biotech, single cell. Also talks about leadership.
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Sep 20, 2023 • 14 tweets • 7 min read
12 (some are free online) Books that I bought for learning (genomic) data science 👇 🧵 #python #rstats #bioinformatics
1/ You need to learn linux command first. Read it for free buff.ly/46f3FQ3
Sep 7, 2023 • 14 tweets • 4 min read
Are protein and RNA correlated? 12 papers and examples 👇 🧵 what do you think?
1/ It is gene-specific, see figure 2D from Quantitative Proteomics of the Cancer Cell Line Encyclopedia buff.ly/3PqSvSL
Jul 28, 2023 • 12 tweets • 4 min read
10 tools/papers related to bulk-RNAseq deconvolution.👇 🧵 #computationalbiology #RNAseq Even in the era of single-cell RNAseq, bulk-RNAseq data are still very valuable.
1. [Benchmarking of cell type deconvolution pipelines for transcriptomics data]()buff.ly/458vpp3
Jul 21, 2023 • 12 tweets • 3 min read
10 FREE #rstats books to uplevel your R skills. 👇 🧵
1/ R Programming for Data Science buff.ly/31g1Y36
Jun 28, 2023 • 18 tweets • 6 min read
16 databases of scRNAseq datasets. 👇 🧵 Reuse them! #singlecell #bioinformatics
1/ [CuratedAtlasQueryR]() is a query interface that allows the programmatic exploration and retrieval of the harmonized, curated and reannotated CELLxGENE single-cell human cell atlas.buff.ly/46DKAIv
Jun 26, 2023 • 14 tweets • 4 min read
Data visualization is key to any data analysis. Make sure you know your data by doing EDA.
12 resources for data visualization 🧵 👇
1/ The R Graph Gallery buff.ly/2lCZxbU
Jun 22, 2023 • 9 tweets • 3 min read
Pathway or gene set enrichment analysis is frequently used in genomic studies. Make sure you understand it with these 8 resources: 👇 🧵
1/ Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges buff.ly/46hQNt5
May 31, 2023 • 18 tweets • 6 min read
16 resources for re-analyzing public expression data. 👇 🧵
1/ buff.ly/3MJfshd RNA meta Analysis has ~26,700 studies (5,717 RNA-Seq and 20,955 Microarray)
May 29, 2023 • 8 tweets • 1 min read
Want to get lucky and be successful? There are four flavors of luck🧵👇
1/ There are four levels of luck: blind luck, luck through motion, luck favoring the prepared mind, and luck finding you through reputation.
1/ False belief: I need to learn fancy machine learning stuff or algorithms for computational biology.
Reality: most of us will only need to learn the data skills to answer biological questions.
Find the roadmap below 👇 🧵
2/ If you are like me, you will not need to develop a reads aligner such as STAR. You will only need to learn how to use those tools. get the reads mapped and get the counts table for DESeq2 for RNAseq. Learn Unix buff.ly/3FITwR1 and RNAseq buff.ly/3mR61mV
Mar 9, 2023 • 11 tweets • 3 min read
Public genomic data and reference data are treasures to researchers. 10 tools to get the data easily from the public repositories.👇 🧵
There was little online material to learn bioinformatics 10 years ago when I started.
I curated ten resources to learn bioinformatics for FREE 🧵👇
1/ Data Analysis for the Life Sciences Series buff.ly/3Z7F1ha by Rafa at DFCI. you can find the courses on Edx buff.ly/3mapP4m
Feb 23, 2023 • 12 tweets • 5 min read
Spatial transcriptome is the next wave after single-cell RNAseq. Resources to bookmark to get into the field 👇 🧵
1/ 8 Review papers:
* [The emerging landscape of spatial profiling technologies](buff.ly/3cwcApw)
* [The expanding vistas of spatial transcriptomics](buff.ly/3m1x9zb)
* [Exploring tissue architecture using spatial transcriptomics](buff.ly/3Sq7Z9f)
Feb 16, 2023 • 6 tweets • 3 min read
People always ask how the protein is expressed if I show the RNA data. Here are the 6 resources for protein data 👇🧵
1/ CPTAC, the biggest database for cancer proteomic.datacommons.cancer.gov/pdc/ python package to access it github.com/PayneLab/cptac
Jan 30, 2023 • 12 tweets • 4 min read
Git is the most popular tool for version control your source code.
But the learning curve can be steep.
Here are the 10 tips for you 🧵 👇 along with learning resource links.
compiled at buff.ly/3Jqxh4W1/ Several basic commands will serve you a long way:
git clone
git add
git commit -m
git push
Those are enough to get you started. To be honest, those are still the most frequent commands I use.
Jan 28, 2023 • 33 tweets • 8 min read
32 resources for (to-be) faculty on salary negotiation, grant writing, funding, and lab management. A thread 🧵 👇
1/ Tips for negotiating salary and startup for newly-hired tenure-track faculty](buff.ly/3Y0GTY0)
Jan 16, 2023 • 11 tweets • 6 min read
1/ If someone tells you that you can learn computation overnight, it is a lie. What I wish I had known 10 years ago with resource links👇🧵 #rstats#computationalbiology2/ Spend time learning Linux commands. Fancy tools can become obsolete tomorrow, and Linux skills persist.
I started with this book linuxcommand.org/tlcl.php#unix
Jan 10, 2023 • 5 tweets • 2 min read
1/ What people think bioinformatician do:
credit: @torstenseemann2/
what I really do 👇
google "ylim without removing data in ggplot" to find coord_cartesian(ylim=c(0, 7)) #rstats every time!
Jan 9, 2023 • 4 tweets • 2 min read
1/
During my years in the lab, I observed that some people hoard their scripts and do not want to share or teach others.
I was the opposite. Although I was a beginner, I taught all that I knew and share my scripts with other lab members who were beginners too.
2/ The results? I learned so much by teaching!
If you want to learn something better, teach it to others.
I can not believe how much I learned by writing my own book too!
Dec 14, 2022 • 17 tweets • 6 min read
15 tools/papers for multi-sample multi-group single-cell RNAseq differential expression analysis 🧵👇
compiled at crazyhottommy.blogspot.com/2022/12/15-too…1/ [An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models](biorxiv.org/content/10.110…) scVI-DE
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