# ![@tangming2005 Avatar](https://lunarcrush.com/gi/w:26/cr:twitter::433559451.png) @tangming2005 Ming "Tommy" Tang

Ming "Tommy" Tang posts on X about shell, rescue, ai, math the most. They currently have [------] followers and [---] posts still getting attention that total [-----] engagements in the last [--] hours.

### Engagements: [-----] [#](/creator/twitter::433559451/interactions)
![Engagements Line Chart](https://lunarcrush.com/gi/w:600/cr:twitter::433559451/c:line/m:interactions.svg)

- [--] Week [------] +89%
- [--] Month [-------] -35%
- [--] Months [-------] +82%
- [--] Year [-------] -29%

### Mentions: [--] [#](/creator/twitter::433559451/posts_active)
![Mentions Line Chart](https://lunarcrush.com/gi/w:600/cr:twitter::433559451/c:line/m:posts_active.svg)

- [--] Week [--] +59%
- [--] Month [---] +16%
- [--] Months [---] +186%
- [--] Year [---] +323%

### Followers: [------] [#](/creator/twitter::433559451/followers)
![Followers Line Chart](https://lunarcrush.com/gi/w:600/cr:twitter::433559451/c:line/m:followers.svg)

- [--] Week [------] +0.27%
- [--] Month [------] +0.83%
- [--] Months [------] +7.50%
- [--] Year [------] +20%

### CreatorRank: [-------] [#](/creator/twitter::433559451/influencer_rank)
![CreatorRank Line Chart](https://lunarcrush.com/gi/w:600/cr:twitter::433559451/c:line/m:influencer_rank.svg)

### Social Influence

**Social category influence**
[technology brands](/list/technology-brands)  6.71% [stocks](/list/stocks)  2.01% [finance](/list/finance)  2.01% [social networks](/list/social-networks)  0.67%

**Social topic influence**
[shell](/topic/shell) 7.38%, [rescue](/topic/rescue) 2.01%, [ai](/topic/ai) 1.34%, [math](/topic/math) 1.34%, [fine](/topic/fine) 1.34%, [if you](/topic/if-you) 1.34%, [youll be](/topic/youll-be) 1.34%, [rna](/topic/rna) 1.34%, [how to](/topic/how-to) 1.34%, [back to](/topic/back-to) 1.34%

**Top accounts mentioned or mentioned by**
[@wendy_wu123](/creator/undefined) [@wendywu123](/creator/undefined) [@valentinesvenssonp159305684](/creator/undefined) [@gamerphildoc](/creator/undefined) [@bzdyelnik](/creator/undefined) [@siam_01](/creator/undefined) [@steen_dr](/creator/undefined) [@iammichaelgrier](/creator/undefined) [@neuroai_nexus](/creator/undefined) [@kristia02459639](/creator/undefined)

**Top assets mentioned**
[FilesCoins Power Cu (FILECOIN)](/topic/files) [Alphabet Inc Class A (GOOGL)](/topic/$googl) [CVS Health Corp (CVS)](/topic/cvs) [UiPath, Inc. (PATH)](/topic/$path)
### Top Social Posts
Top posts by engagements in the last [--] hours

"3/ Real speed isnt magic. Its mastering small things that compoundlike navigating the file system without thinking. Let me show you"  
[X Link](https://x.com/tangming2005/status/2023045921081376780)  2026-02-15T14:45Z 43.4K followers, [----] engagements


"I was featured in The Data Wire by Pure Storage. Data challenge comes before the algorithm/AI challenge"  
[X Link](https://x.com/tangming2005/status/2019422025513857304)  2026-02-05T14:45Z 43.4K followers, [----] engagements


"Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer https://www.cell.com/cancer-cell/fulltext/S1535-6108(25)00537-9 https://www.cell.com/cancer-cell/fulltext/S1535-6108(25)00537-9"  
[X Link](https://x.com/tangming2005/status/2019791987889889390)  2026-02-06T15:15Z 43.3K followers, [----] engagements


"3/ Most errors are simple to fix: Missing library Install it. Version mismatch Update. Syntax error Fix the typo. These are mechanical. And this is exactly where AI agents shine"  
[X Link](https://x.com/tangming2005/status/2020504161004273999)  2026-02-08T14:25Z 43.3K followers, [---] engagements


"1/ Think Unix is old-school Heres a one-liner counting columns in a TSV file. Fast. Reliable. Elegant"  
[X Link](https://x.com/tangming2005/status/2020509188435353815)  2026-02-08T14:45Z 43.4K followers, [----] engagements


"8/ -n lists column numbers and names. -t tells csvcut that the file is tab-delimited. Much safer than hacking with cut"  
[X Link](https://x.com/tangming2005/status/2020509270731874399)  2026-02-08T14:45Z 43.3K followers, [--] engagements


"9/ Real-world case: I once got a malformed TSV with invisible carriage returns. awk spotted it instantly. GUI tools missed it"  
[X Link](https://x.com/tangming2005/status/2020509282379424065)  2026-02-08T14:45Z 43.3K followers, [--] engagements


"6/ Things I'll say out loud: Research code and production code are different. Stop telling bioinformaticians to write "production-ready" pipelines. We're answering questions not shipping products"  
[X Link](https://x.com/tangming2005/status/2020864091959738491)  2026-02-09T14:15Z 43.3K followers, [--] engagements


"7/ Statistical significance doesn't mean biological plausibility. And AI can refactor your working code beautifully -- but verify everything it generates from scratch. Especially R"  
[X Link](https://x.com/tangming2005/status/2020864103712190582)  2026-02-09T14:15Z 43.3K followers, [--] engagements


"13/ Find your community Youre not alone Join: 🔹 BioStars 🔹 SEQanswers 🔹 Twitter/X bioinformatics communities http://seqanswers.com/ http://www.biostars.org/ http://seqanswers.com/ http://www.biostars.org/"  
[X Link](https://x.com/tangming2005/status/2020871733897736463)  2026-02-09T14:45Z 43.3K followers, [---] engagements


"14/ Final Thoughts Want to get started ✅ Install Linux ✅ Learn bash & Python/R ✅ Try real-world datasets You will be amazed at what you can do I read the original article when it came out [--] years ago It makes so much sense today. https://www.nature.com/articles/nbt.2740 https://www.nature.com/articles/nbt.2740"  
[X Link](https://x.com/tangming2005/status/2020871745759223832)  2026-02-09T14:45Z 43.3K followers, [---] engagements


"@wendy_wu123 I have not read any fictions recently. My friend recommended Atlas Shrugged. For non-fiction I recommend the almanack of Naval Ravikant https://www.navalmanack.com https://www.navalmanack.com"  
[X Link](https://x.com/tangming2005/status/2021571091756425602)  2026-02-11T13:04Z 43.3K followers, [--] engagements


"🧵The most underrated superpower in science: Bioinformaticians and wet biologists working together. Heres why it matters"  
[X Link](https://x.com/tangming2005/status/2021588811684417811)  2026-02-11T14:15Z 43.3K followers, [----] engagements


"ICE: robust detection of cellular senescence from weak single-cell signatures using imputation-based marker refinement https://link.springer.com/article/10.1186/s13059-026-03997-0 https://link.springer.com/article/10.1186/s13059-026-03997-0"  
[X Link](https://x.com/tangming2005/status/2021603913745809862)  2026-02-11T15:15Z 43.3K followers, [----] engagements


"3/ So should you integrate It depends on your question. Are you studying shared biology or donor-specific differences"  
[X Link](https://x.com/tangming2005/status/2021958776107258009)  2026-02-12T14:45Z 43.3K followers, [---] engagements


"4/ Use integration when: You assume shared cell types across samples You want a common map https://bioconductor.org/books/3.20/OSCA.multisample/integrating-datasets.html#no-correction https://bioconductor.org/books/3.20/OSCA.multisample/integrating-datasets.html#no-correction"  
[X Link](https://x.com/tangming2005/status/2021958787863879917)  2026-02-12T14:45Z 43.3K followers, [---] engagements


"6/ Example 1: You want to count B cells across donors integrate You want to find activated B cells in COVID dont integrate read details here https://substack.com/@valentinesvensson/p-159305684 https://substack.com/@valentinesvensson/p-159305684"  
[X Link](https://x.com/tangming2005/status/2021958811754672168)  2026-02-12T14:45Z 43.3K followers, [---] engagements


"7/ Integration helps when building a reference atlas Consistent clusters Easy annotation Shared UMAPs But it may hide subtle state shifts"  
[X Link](https://x.com/tangming2005/status/2021958823758672133)  2026-02-12T14:45Z 43.3K followers, [---] engagements


"Daily Quote https://daily-quote-app-mu.vercel.app/ https://daily-quote-app-mu.vercel.app/"  
[X Link](https://x.com/tangming2005/status/2022282156270313918)  2026-02-13T12:10Z 43.4K followers, [---] engagements


"4/ Now consider CITE-seq: protein counts at the same cell resolution. But protein counts are noisy. Why"  
[X Link](https://x.com/tangming2005/status/2022313632894484894)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"5/ Because unbound antibodies can sneak into droplets. They float around and get encapsulated. This creates ambient ADT noise"  
[X Link](https://x.com/tangming2005/status/2022313644542021927)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"7/ Learning each data type is hard. Its tempting to chase every new method. But theres a better way"  
[X Link](https://x.com/tangming2005/status/2022313668072116473)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"8/ Stick to what doesnt change. Unix commands have worked for 50+ years. Statistics still rule the game. Linear algebra is everywhere"  
[X Link](https://x.com/tangming2005/status/2022313679770034591)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"9/ Gene expression matrix Thats linear algebra. Normalization Statistical modeling. Data wrangling Unix 101"  
[X Link](https://x.com/tangming2005/status/2022313691564458450)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"10/ Start with the basics: Learn shell scripting Get comfortable with matrix math Understand core statistical models"  
[X Link](https://x.com/tangming2005/status/2022313703316832406)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"12/ It takes time to learn a new data type. But youll be fine if you focus on the foundations"  
[X Link](https://x.com/tangming2005/status/2022313726783971630)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"13/ Key takeaways: Bioinformatics tech will keep evolving Data types differso do methods Foundations like Unix stats and math dont change"  
[X Link](https://x.com/tangming2005/status/2022313738460893564)  2026-02-13T14:15Z 43.4K followers, [---] engagements


"2/ CellRank solves this by building a cell-cell transition matrix. It creates a Markov chain that predicts where cells are going based on RNA velocity and transcriptomic similarity"  
[X Link](https://x.com/tangming2005/status/2022321162320327065)  2026-02-13T14:45Z 43.4K followers, [---] engagements


"3/ RNA velocity estimates the direction each cell is moving. CellRank uses that plus gene expression similarity to figure out: Which cells are terminal states How do lineages form"  
[X Link](https://x.com/tangming2005/status/2022321174152360313)  2026-02-13T14:45Z 43.4K followers, [---] engagements


"R is slow in plotting tens of thousands of points. How to speed up for a million cell scRNAseq data check out scattermore https://github.com/exaexa/scattermore https://github.com/exaexa/scattermore"  
[X Link](https://x.com/tangming2005/status/2021596350153146767)  2026-02-11T14:45Z 43.4K followers, [----] engagements


"9/ Action items: If you're analyzing differentiation or disease progression consider CellRank Combine velocity with pseudotime or experimental time for better results Check out the Nature Protocols paper for detailed workflows"  
[X Link](https://x.com/tangming2005/status/2022321244671213746)  2026-02-13T14:45Z 43.4K followers, [---] engagements


"3/ At a biotech startup we learned this the hard way. Heres what I took from a panel and years of practice. The essentials: Governance Management Metadata Team dynamics Tool choices"  
[X Link](https://x.com/tangming2005/status/2022675988270977334)  2026-02-14T14:15Z 43.4K followers, [---] engagements


"4/ Start with data governance. Access control. Versioning. Basic security. Do it early. Fixing leaks later costs 10x more"  
[X Link](https://x.com/tangming2005/status/2022676000065360245)  2026-02-14T14:15Z 43.4K followers, [--] engagements


"5/ Cloud is greatbut only if you use it right. Define who sees what. Set folder rules. Use Google or AWS security playbooks. Theyre free and solid"  
[X Link](https://x.com/tangming2005/status/2022676011834577094)  2026-02-14T14:15Z 43.4K followers, [--] engagements


"7/ Spreadsheets are fineuntil they arent. Start smart: Female not F No weird characters Train your wet lab team. Seriously"  
[X Link](https://x.com/tangming2005/status/2022676035352039696)  2026-02-14T14:15Z 43.4K followers, [--] engagements


"8/ Youll accrue technical debt. Thats fine. If someone curses your naming scheme [--] years from now congrats. You survived"  
[X Link](https://x.com/tangming2005/status/2022676046999662754)  2026-02-14T14:15Z 43.4K followers, [--] engagements


"19/ Startups die by disorganized data. Dont be one of them. Fix your foundation nowbefore the chaos scales"  
[X Link](https://x.com/tangming2005/status/2022676176075116672)  2026-02-14T14:15Z 43.4K followers, [--] engagements


"20/ Have you seen data disasters in biotech How did you fix itor not Reply and lets trade war stories"  
[X Link](https://x.com/tangming2005/status/2022676187722715237)  2026-02-14T14:15Z 43.4K followers, [---] engagements


"7/ Look for tools with active communities. Seurat and Scanpy stick around because people use them update them and answer questions"  
[X Link](https://x.com/tangming2005/status/2023038430624805010)  2026-02-15T14:15Z 43.4K followers, [--] engagements


"8/ My approach: Test [--] tools on a data subset. See which one fits. Then commit. No month-long testing marathons"  
[X Link](https://x.com/tangming2005/status/2023038442247242219)  2026-02-15T14:15Z 43.4K followers, [--] engagements


"1/ When I started bioinformatics I watched a postdoc type like a hacker in a movie. Lightning fast. No mouse. Just keys"  
[X Link](https://x.com/tangming2005/status/2023045897266041192)  2026-02-15T14:45Z 43.4K followers, [----] engagements


"2/ I thought: Damn. Ill never be that fast. Years later I realized the truth. They were just using cd mkdir and tab-complete"  
[X Link](https://x.com/tangming2005/status/2023045909345698012)  2026-02-15T14:45Z 43.4K followers, [----] engagements


"5/ Want to go to your home directory Simple: cd No Just cd"  
[X Link](https://x.com/tangming2005/status/2023045944527540276)  2026-02-15T14:45Z 43.4K followers, [---] engagements


"6/ Need to go back to your previous folder Use: cd - It toggles between your current and last directory. Like a "Back" button for your terminal"  
[X Link](https://x.com/tangming2005/status/2023045956137369911)  2026-02-15T14:45Z 43.4K followers, [---] engagements


"1/ If you're in bioinformatics you're staring at matrices all day. RNA-seq Gene x sample. scRNA-seq Gene x cell. Everything is a matrix. But I never learned how to think in matrices. And I regret it"  
[X Link](https://x.com/tangming2005/status/2021951186757464403)  2026-02-12T14:15Z 43.4K followers, [----] engagements


"12/ Want to create parent directories in one shot mkdir -p project/data/raw No error if parent folders dont exist. It just works"  
[X Link](https://x.com/tangming2005/status/2023046027385938011)  2026-02-15T14:45Z 43.4K followers, [---] engagements


"13/ Key takeaways: Most speed in the terminal is repetition mastered Shortcuts speed Its not wizardry. Its a habit"  
[X Link](https://x.com/tangming2005/status/2023046039083835559)  2026-02-15T14:45Z 43.4K followers, [---] engagements


"Precision treatment with artificial intelligence assisted subtyping enhances therapeutic efficacy in HR+/HER2 breast cancer: The LINUXtrial https://www.cell.com/cancer-cell/fulltext/S1535-6108(25)00496-9 https://www.cell.com/cancer-cell/fulltext/S1535-6108(25)00496-9"  
[X Link](https://x.com/tangming2005/status/2023415850221601056)  2026-02-16T15:15Z 43.4K followers, [----] engagements


"8/ Every wasted hour Ive had in bioinformatics traces back to one thing: ignoring data cleaning. Get this step right and the rest flows"  
[X Link](https://x.com/tangming2005/status/1958155917461176699)  2025-08-20T13:15Z 40.4K followers, [--] engagements


"9/ Key takeaways: Metadata is always messier than you think. Standardize early. Inspect everything. Cleaning isnt busyworkits survival"  
[X Link](https://x.com/tangming2005/status/1958155929213644961)  2025-08-20T13:15Z 40.4K followers, [--] engagements


"Unlock your bioinformatics potential 🌟 Discover why mastering both Python and R can elevate your data visualization and analysis skills. Dive into the world of code 💻 #Bioinformatics"  
[X Link](https://x.com/tangming2005/status/1958344619953135805)  2025-08-21T01:45Z 40.4K followers, [----] engagements


"1/ a single job opening receives [----] applications. (I am not kidding). How to stand out Most bioinformatics CVs look the same: Python R RNA-seq pipelines. But hiring managers dont care about skills on paper. They care about proof. 🧵"  
[X Link](https://x.com/tangming2005/status/1958880597717524722)  2025-08-22T13:15Z 40.6K followers, 11.3K engagements


"5/ Two tools cover 90% of bioinformatics plots: ggplot2 for almost everything. ComplexHeatmap for serious heatmaps"  
[X Link](https://x.com/tangming2005/status/1958895743558984140)  2025-08-22T14:15Z 40.4K followers, [---] engagements


"6/ But heres the catch: plots fall apart if your data isnt shaped right. The hidden skill is restructuring data into a usable format"  
[X Link](https://x.com/tangming2005/status/1958895755307229401)  2025-08-22T14:15Z 40.4K followers, [---] engagements


"1/ Biology is no longer just about pipettes and Petri dishes. Your most powerful lab tool is hidden in plain sight: a keyboard. Learning to code can transform not just your researchbut your career"  
[X Link](https://x.com/tangming2005/status/1959242981363642675)  2025-08-23T13:15Z 40.5K followers, [----] engagements


"5/ Rule 2: Take it one step at a time. Your dataset may have millions of rows. Dont panic. Start by reading the file. Then filter. Then plot. Tiny victories compound into breakthroughs"  
[X Link](https://x.com/tangming2005/status/1959243029807866269)  2025-08-23T13:15Z 40.4K followers, [---] engagements


"6/ Rule 3: Focus on one thing. I once jumped between Python R and MATLAB. I ended up confused and slower. When I finally stuck with R the learning curve flattened. Depth beats breadthespecially at the beginning"  
[X Link](https://x.com/tangming2005/status/1959243041707037040)  2025-08-23T13:15Z 40.4K followers, [---] engagements


"@GamerPhilDoc Digital centrifuge. Like that analogy"  
[X Link](https://x.com/tangming2005/status/1959414406111998369)  2025-08-24T00:36Z 40.4K followers, [--] engagements


"Applied Computational Genomics Course at UU: Spring [----] by the almighty Aaron Quinlan author of bedtools and many other great tools for genomics analysis. https://github.com/quinlan-lab/applied-computational-genomics https://github.com/quinlan-lab/applied-computational-genomics"  
[X Link](https://x.com/tangming2005/status/1959982858740887733)  2025-08-25T14:15Z 40.7K followers, 15.9K engagements


""just like Madame Gazelle in Peppa hooray" she then started to count in English: "21 [--] [--] 28." I have no idea how she learned those because we speak Chinese at home"  
[X Link](https://x.com/tangming2005/status/1960169936036532517)  2025-08-26T02:38Z 40.5K followers, [--] engagements


"pretty interesting tool: Oxbow makes genomic data ready for high-performance analytics. https://oxbow.readthedocs.io/en/latest/ https://oxbow.readthedocs.io/en/latest/"  
[X Link](https://x.com/tangming2005/status/1960345246157672554)  2025-08-26T14:15Z 40.7K followers, [----] engagements


"🧵 If youre doing bioinformatics by hand youre burning time youll never get back. 1/ Every biologist has done this: Copying a file name pasting it into the terminal running one command. Then doing it again. And again. Hours gone. Nothing scalable"  
[X Link](https://x.com/tangming2005/status/1961054931038908475)  2025-08-28T13:15Z 40.6K followers, [----] engagements


"3/ Level 1: Manual Execution This is where most start. Run each command line by line. Edit file names by hand. Rerun the same script [--] times. It feels like progress but its not. Its slow error-prone and breaks the moment your dataset grows"  
[X Link](https://x.com/tangming2005/status/1961054955638509775)  2025-08-28T13:15Z 40.6K followers, [---] engagements


"4/ Level 2: Automating with Bash Here you start letting the computer work for you. Instead of: fastqc sample1.fastq fastqc sample2.fastq fastqc sample3.fastq You write: for f in *.fastq; do fastqc $f; done One command. All files. This is the first taste of freedom"  
[X Link](https://x.com/tangming2005/status/1961054967751733551)  2025-08-28T13:15Z 40.6K followers, [---] engagements


"11/ Be ready to fail. Computational biology is trial and error. Your code will crash. Your analysis will mislead. The lesson is in the failure"  
[X Link](https://x.com/tangming2005/status/1961779817617174560)  2025-08-30T13:15Z 40.6K followers, [---] engagements


"12/ Big data = big traps. Random noise can look like signal. Always ask: does this make biological sense Skepticism is your superpower"  
[X Link](https://x.com/tangming2005/status/1961779829780693460)  2025-08-30T13:15Z 40.6K followers, [---] engagements


"4/ But heres the truth: modern biology runs on code. Pipettes alone cant handle the questions we now ask"  
[X Link](https://x.com/tangming2005/status/1962866919318704382)  2025-09-02T13:15Z 40.7K followers, [---] engagements


"5/ It brings order. Linnaeus once classified species by hand. Now Gene Ontology Ensembl KEGG do it at scale"  
[X Link](https://x.com/tangming2005/status/1962866931146641752)  2025-09-02T13:15Z 40.7K followers, [---] engagements


"10/ Apply to a vector: str_replace(ensembl_ids ".0-9+" "") Now every version number disappears"  
[X Link](https://x.com/tangming2005/status/1963236936988213384)  2025-09-03T13:45Z 40.8K followers, [---] engagements


"11/ Want only IDs that start with ENSG str_subset(ensembl_ids "ENSG") The anchors at the start"  
[X Link](https://x.com/tangming2005/status/1963236948778381689)  2025-09-03T13:45Z 41.2K followers, [---] engagements


"2. The International Human Epigenome Consortium (IHEC) epigenome data portal http://epigenomesportal.ca/ihec/index.htmlas=1 http://epigenomesportal.ca/ihec/index.htmlas=1"  
[X Link](https://x.com/tangming2005/status/1963969146032697664)  2025-09-05T14:15Z 40.8K followers, [---] engagements


"3. Blueprint epigenome http://dcc.blueprint-epigenome.eu/#/home http://dcc.blueprint-epigenome.eu/#/home"  
[X Link](https://x.com/tangming2005/status/1963969157814526427)  2025-09-05T14:15Z 40.8K followers, [---] engagements


"7. ChIP-Atlas An integrative comprehensive database to explore public Epigenetic dataset including ChIP-Seq DNase-Seq ATAC-Seq and Bisulfite-Seq data: ChIP-Atlas covers almost all public data archived in Sequence Read Archive of NCBI http://chip-atlas.org/ http://chip-atlas.org/"  
[X Link](https://x.com/tangming2005/status/1963969205797310509)  2025-09-05T14:15Z 40.7K followers, [----] engagements


"8. Fantom5 https://fantom.gsc.riken.jp/5/ https://fantom.gsc.riken.jp/5/"  
[X Link](https://x.com/tangming2005/status/1963969217788858684)  2025-09-05T14:15Z 40.8K followers, [----] engagements


"7/ Search: "differential isoform RNAseq Bioconductor" Youll find: * IsoformSwitchAnalyzeR * DEXSeq * EBSeq"  
[X Link](https://x.com/tangming2005/status/1965041276228944142)  2025-09-08T13:15Z 40.8K followers, [--] engagements


"8/ Or ask ChatGPT. Ask smart targeted questions. Most of the time youll find you dont need to start from scratch"  
[X Link](https://x.com/tangming2005/status/1965041288056852940)  2025-09-08T13:15Z 40.8K followers, [--] engagements


"9/ Takeaways: Save time by reusing trusted tools. Verify the tools credibility. Know when to build from scratchand when not to"  
[X Link](https://x.com/tangming2005/status/1965041299943559421)  2025-09-08T13:15Z 40.8K followers, [--] engagements


"4/ Over time you start noticing things: Bad FASTQ files before the aligner screams Inconsistent metadata that ruins downstream stats When a PCA plot lies These are scars earned not shortcuts taken"  
[X Link](https://x.com/tangming2005/status/1965403620494688652)  2025-09-09T13:15Z 40.8K followers, [---] engagements


"5/ You build intuition. Why this QC step matters When an outlier is noise vs. signal How to debug a DESeq2 error with StackOverflow (now with LLM) And it only comes with mileage"  
[X Link](https://x.com/tangming2005/status/1965403632335237472)  2025-09-09T13:15Z 40.8K followers, [---] engagements


"9/ If you feel behindgood. That means youre aware. Keep going. Learn every week. [--] years from now youll be shocked how far youve come"  
[X Link](https://x.com/tangming2005/status/1965403680116801872)  2025-09-09T13:15Z 40.8K followers, [---] engagements


"10/ Key takeaways: Time is your biggest advantage Experience builds intuition Dont rush; compound learning daily Mistakes teach more than success"  
[X Link](https://x.com/tangming2005/status/1965403691932156217)  2025-09-09T13:15Z 40.8K followers, [---] engagements


"13/ Better strategies: Use noise-aware statistical models that account for UMI noise and sequencing depth variation directly"  
[X Link](https://x.com/tangming2005/status/1966128505173004571)  2025-09-11T13:15Z 41.2K followers, [--] engagements


"14/ CS-CORE: Explicitly models sequencing depth and measurement errors to estimate unbiased gene-gene correlations"  
[X Link](https://x.com/tangming2005/status/1966128516900274672)  2025-09-11T13:15Z 41.2K followers, [--] engagements


"4. ImaGEO: Integrative Meta-Analysis of GEO Data https://imageo.genyo.es/ https://imageo.genyo.es/"  
[X Link](https://x.com/tangming2005/status/1966135961039073762)  2025-09-11T13:45Z 40.8K followers, [---] engagements


"5. Gemma https://gemma.msl.ubc.ca/home.html https://gemma.msl.ubc.ca/home.html"  
[X Link](https://x.com/tangming2005/status/1966135972745335161)  2025-09-11T13:45Z 40.8K followers, [---] engagements


"1. Canva it can also make a nice logo. I made my Linkedin banner with it. https://www.canva.com/graphs/flowcharts/ https://www.canva.com/graphs/flowcharts/"  
[X Link](https://x.com/tangming2005/status/1970846956433133925)  2025-09-24T13:45Z 40.9K followers, [---] engagements


"2. Figma recently bought by Adobe https://www.figma.com/templates/flowchart-maker/ https://www.figma.com/templates/flowchart-maker/"  
[X Link](https://x.com/tangming2005/status/1970846968302997855)  2025-09-24T13:45Z 40.9K followers, [---] engagements


"3. Adobe illustrator"  
[X Link](https://x.com/tangming2005/status/1970846980302942209)  2025-09-24T13:45Z 40.9K followers, [---] engagements


"(TPCPA) a proteomic resource that provides proteome-scale quantifications of [---] tumors across [--] cancer types in a unified manner for discovering tumor biology biomarkers and therapeutic targets. https://hgserver1.amc.nl/cgi-bin/r2/main.cgidscope=TCPA&option=about_dscope https://hgserver1.amc.nl/cgi-bin/r2/main.cgidscope=TCPA&option=about_dscope"  
[X Link](https://x.com/tangming2005/status/1971216889629245781)  2025-09-25T14:15Z 41K followers, [----] engagements


"1/ You launched a long-running program. And forgot to use screen or tmux. Now you're terrified to close your terminal. Ive been there. Heres how to rescue it like a pro"  
[X Link](https://x.com/tangming2005/status/1971571740854911025)  2025-09-26T13:45Z 40.9K followers, [----] engagements


"5/ Step 2: Resume it in the background Type: bg This will resume the job but now it runs in the background. Still tied to your shellfor now"  
[X Link](https://x.com/tangming2005/status/1971571789265576322)  2025-09-26T13:45Z 40.9K followers, [--] engagements


"6/ Step 3: Disown the job Type: disown %1 This detaches the job from your shell. You can now safely close the terminalbut you still cant interact with it yet"  
[X Link](https://x.com/tangming2005/status/1971571801106096175)  2025-09-26T13:45Z 40.9K followers, [--] engagements


"7/ Step 4: Start a screen session screen -S rescue This opens a fresh terminal inside a screen session. This is where youll move the process"  
[X Link](https://x.com/tangming2005/status/1971571812917272809)  2025-09-26T13:45Z 40.9K followers, [--] engagements


"10/ Note: reptyr might not be installed by default. On Ubuntu/Debian: sudo apt install reptyr And it may require some permissions (ptrace_scope). See: https://github.com/nelhage/reptyr#ptrace_scope https://github.com/nelhage/reptyr#ptrace_scope"  
[X Link](https://x.com/tangming2005/status/1971571848552026190)  2025-09-26T13:45Z 40.9K followers, [--] engagements


"11/ Bonus tip: Use screen -r rescue to reattach later. Or screen -ls to list all sessions. Want to make it even more robust Start using tmux or screen by default. Always"  
[X Link](https://x.com/tangming2005/status/1971571860526772565)  2025-09-26T13:45Z 40.9K followers, [--] engagements


"@bzdyelnik sorry the Docker image is not compatible with your M3 chip on mac"  
[X Link](https://x.com/tangming2005/status/1971781225909268672)  2025-09-27T03:37Z 40.9K followers, [--] engagements


"2/ With awk: awk 'gsub(/pattern/ "replace" $5)1' input.txt gsub = global substitution $5 = only apply to column [--] [--] = shorthand to print the line"  
[X Link](https://x.com/tangming2005/status/1971934122072510946)  2025-09-27T13:45Z 41K followers, [--] engagements


"3/ Example: awk 'gsub("chr" "" $5)1' input.txt Removes "chr" from just column [--]. Leaves the rest untouched"  
[X Link](https://x.com/tangming2005/status/1971934133959200908)  2025-09-27T13:45Z 41K followers, [--] engagements


"7/ Heres the philosophy: Dont touch what doesnt need to change. Surgical edits. Column-aware. Whether in UNIX or R"  
[X Link](https://x.com/tangming2005/status/1971934181178650949)  2025-09-27T13:45Z 41K followers, [--] engagements


"8/ Real-world use case Say you downloaded a VCF or BED file and one column has chr1 chr2 etc. But your tool expects [--] [--] etc. Fixing just column 1: awk 'gsub(/chr/ "" $1)1' file.bed clean.bed"  
[X Link](https://x.com/tangming2005/status/1971934192905961526)  2025-09-27T13:45Z 41K followers, [--] engagements


"1/"I have a presentation tomorrow." If you've ever collaborated with wet lab scientists as a bioinformatician youve heard this. And died inside a little"  
[X Link](https://x.com/tangming2005/status/1972288945154294163)  2025-09-28T13:15Z 41K followers, [----] engagements


"10/ So what do you do You lean into what you do know: The biology The patient history The sample metadata The context of the trial"  
[X Link](https://x.com/tangming2005/status/1972651456642920675)  2025-09-29T13:15Z 41K followers, [--] engagements


"11/ This isnt big data. Its precious noisy human data. Understanding the story behind each sample is more powerful than any algorithm"  
[X Link](https://x.com/tangming2005/status/1972651468324045300)  2025-09-29T13:15Z 41K followers, [--] engagements


"3/ You can find the video classes on Coursera https://www.bioinformaticsalgorithms.org/ https://www.bioinformaticsalgorithms.org/"  
[X Link](https://x.com/tangming2005/status/1973021319714459966)  2025-09-30T13:45Z 41K followers, [---] engagements


"4/ not a course biostar Handbook but Istvan (creator of the uses it in his class at Penn State I contributed a ChIP-seq chapter in [----] https://www.biostarhandbook.com/index.html http://biostars.org https://www.biostarhandbook.com/index.html http://biostars.org"  
[X Link](https://x.com/tangming2005/status/1973021331525623905)  2025-09-30T13:45Z 41K followers, [---] engagements


"1/ Whats a BED file In its simplest form Just [--] columns: chromosome start end Thats it. But its the backbone of genomic data. Read here for UCSC definition of bed files https://genome.ucsc.edu/FAQ/FAQformat.html#format1 https://genome.ucsc.edu/FAQ/FAQformat.html#format1"  
[X Link](https://x.com/tangming2005/status/1973383674986111330)  2025-10-01T13:45Z 41.1K followers, [--] engagements


"2/ Want to represent genomic intervals You use BED. Its how tools like bedtools IGV and UCSC talk. Simplebut strict"  
[X Link](https://x.com/tangming2005/status/1973383687057317909)  2025-10-01T13:45Z 41.1K followers, [--] engagements


"5/ Exploratory Data Analysis (EDA) isnt extra. Its survival. Boxplots. Histograms. PCA. Use them all"  
[X Link](https://x.com/tangming2005/status/1973746096913731612)  2025-10-02T13:45Z 41.1K followers, [--] engagements


"6/ For genomics: Never trust variant calls blindly. Fire up IGV. Zoom into those BAM files. What looks like a somatic mutation may be a mapping mess"  
[X Link](https://x.com/tangming2005/status/1973746108661919939)  2025-10-02T13:45Z 41.1K followers, [--] engagements


"7/ In ChIP-seq visualize peaks on a genome browser. Off-target antibodies Duplicate artifacts Black-listed regions They all look different in IGV"  
[X Link](https://x.com/tangming2005/status/1973746120397664740)  2025-10-02T13:45Z 41.1K followers, [--] engagements


"13/ EDA saves time. It saves embarrassment. And it makes you a better scientist not just a better coder"  
[X Link](https://x.com/tangming2005/status/1973746190807441911)  2025-10-02T13:45Z 41.1K followers, [--] engagements


"14/ Key takeaways: Trust your gut when something feels off Visualize before and after every major step Use IGV PCA boxplots histograms Dont assumecheck"  
[X Link](https://x.com/tangming2005/status/1973746202555609451)  2025-10-02T13:45Z 41.1K followers, [--] engagements


"2/ In [----] if you had a problem you went to Biostars or StackOverflow. You waited days. Or you searched for hours"  
[X Link](https://x.com/tangming2005/status/1974825672242782283)  2025-10-05T13:15Z 41.1K followers, [--] engagements


"3/ Now You ask ChatGPT Claude or Gemini. You get a decent answer in seconds. Thats not magic. Thats leverage"  
[X Link](https://x.com/tangming2005/status/1974825683861082370)  2025-10-05T13:15Z 41.1K followers, [--] engagements


"I have to confess: I use AI for most of my posts. but that does not make it less value You get to have the ideas/first draft first for ChatGPT to improve on"  
[X Link](https://x.com/tangming2005/status/1975418530221990099)  2025-10-07T04:30Z 41.1K followers, [----] engagements


"1/ Bioinformatics takes years to master. Not because its hard. But because so much of what matters no one writes down. Let me explain"  
[X Link](https://x.com/tangming2005/status/1975550443653898393)  2025-10-07T13:15Z 41.2K followers, 33.4K engagements


"7/ You dont trust data blindly. You run PCA and check sample labels. If control and knockdown mix in PCA space Somethings wrong"  
[X Link](https://x.com/tangming2005/status/1975550514776691043)  2025-10-07T13:15Z 41.1K followers, [----] engagements


"8/ You learn that when a variant isn't real. Low Allel frequency PCR bias. Maybe a mapping error. That mutation calls are only as good as your filters. That nothing replaces a manual check in IGV"  
[X Link](https://x.com/tangming2005/status/1975550526420062654)  2025-10-07T13:15Z 41.1K followers, [----] engagements


"In a rapidly changing AI landscape how do you stay relevant Focus on timeless skills: [--]. the ability to learn and have the curiosity to learn"  
[X Link](https://x.com/tangming2005/status/1975756145336987717)  2025-10-08T02:52Z 41.1K followers, [----] engagements


"Always stay curious. Keep up-to-date with the latest advancements in AI tools: Perplexity Cursor Replit Codex Claude Code and OpenAI Agent Builder. How Follow people at the forefront of AI advancements. It's a great use of social media (X/LinkedIn)"  
[X Link](https://x.com/tangming2005/status/1975756157055869170)  2025-10-08T02:52Z 41.1K followers, [---] engagements


"2/ A log2FC of [--] means 2x up or down. Its common to use this as a cutoff in RNA-seq. But guess what Sometimes a 50% change (log2FC 0.58) is biologically meaningfulespecially for dosage-sensitive genes"  
[X Link](https://x.com/tangming2005/status/1975912868009943204)  2025-10-08T13:15Z 41.1K followers, [---] engagements


"3/ Take transcription factors. A modest drop in expression can disrupt regulatory networks. A small increase can trigger a cascade. Context matters"  
[X Link](https://x.com/tangming2005/status/1975912879766540673)  2025-10-08T13:15Z 41.1K followers, [---] engagements


"12/ Always go back to the genome browser. Visualize your bigwig. Zoom into the peaks. Some truths are in the noise"  
[X Link](https://x.com/tangming2005/status/1975912985572048969)  2025-10-08T13:15Z 41.1K followers, [---] engagements


"13/ Bioinformatics isnt about being strict. Its about being smart. Knowing when to trust the defaults and when to question them"  
[X Link](https://x.com/tangming2005/status/1975912997311947004)  2025-10-08T13:15Z 41.1K followers, [---] engagements


"I was featured in The Data Wire by Pure Storage. Data challenge comes before the algorithm/AI challenge"  
[X Link](https://x.com/tangming2005/status/1976157573318693344)  2025-10-09T05:27Z 41.2K followers, [----] engagements


"Ever wondered why analyzing RNA-seq data feels like walking through a fog with [-----] dimensions Lets talk about the curse of dimensionality in bioinformaticsand why its not just a math problem its a biological one. 🧵"  
[X Link](https://x.com/tangming2005/status/1976275221088018810)  2025-10-09T13:15Z 41.2K followers, 14.7K engagements


"9/14 ChatGPT Prompt Template: "Im on macOS Ventura R 4.3.0. Trying to install DESeq2 with BiocManager::install(). Got this error: paste. Whats wrong Context matters"  
[X Link](https://x.com/tangming2005/status/1976282875650769319)  2025-10-09T13:45Z 41.2K followers, [--] engagements


"10/14 Nuclear option: Start fresh. R --vanilla # No startup configs install.packages("problematic_pkg") Or use renv/conda for isolated environments"  
[X Link](https://x.com/tangming2005/status/1976282887558434833)  2025-10-09T13:45Z 41.2K followers, [--] engagements


"A human pan-disease blood atlas of the circulating proteome Science https://www.science.org/doi/10.1126/science.adx2678 https://www.science.org/doi/10.1126/science.adx2678"  
[X Link](https://x.com/tangming2005/status/1976652715569914111)  2025-10-10T14:15Z 41.2K followers, 32.6K engagements


"5/ RStudio acting weird after you install a package Session Restart R (or just Cmd/Ctrl + Shift + F10)"  
[X Link](https://x.com/tangming2005/status/1977362442754875400)  2025-10-12T13:15Z 41.2K followers, [--] engagements


"6/ New conda environment not activating as expected Deactivate and reactivate: conda deactivate conda activate myenv Still doesnt work Restart the shell"  
[X Link](https://x.com/tangming2005/status/1977362454448591202)  2025-10-12T13:15Z 41.2K followers, [--] engagements


"7/ Just updated your PATH but your terminal doesn't see it echo $PATH If it's not showing up you probably didnt restart your session or source your profile"  
[X Link](https://x.com/tangming2005/status/1977362466150752678)  2025-10-12T13:15Z 41.2K followers, [---] engagements


"8/ This applies to cloud too. On AWS or GCP If your VMs behaving strangely a simple reboot can fix a hung process or config delay"  
[X Link](https://x.com/tangming2005/status/1977362477940945121)  2025-10-12T13:15Z 41.2K followers, [--] engagements


"11/ Youre not being lazy. Youre being efficient. You can spend [--] hours debugging or [--] seconds restarting. Choose wisely"  
[X Link](https://x.com/tangming2005/status/1977362512854274081)  2025-10-12T13:15Z 41.2K followers, [--] engagements


"12/ Key takeaways: Restart is your first line of defense Dont trust a stale session Reload your shell RStudio conda or even reboot Sometimes the fix is simpler than you think"  
[X Link](https://x.com/tangming2005/status/1977362524459901075)  2025-10-12T13:15Z 41.2K followers, [--] engagements


"9/ You check for batch effects. You wonder if a different normalization method changes the conclusion. Spoiler: it might"  
[X Link](https://x.com/tangming2005/status/1977724885020594536)  2025-10-13T13:15Z 41.2K followers, [---] engagements


"10/ You start with DESeq2. Try edgeR. Maybe limma-voom. The results overlap but differences remain. Thats the art: building confidence across tools"  
[X Link](https://x.com/tangming2005/status/1977724896596906416)  2025-10-13T13:15Z 41.2K followers, [---] engagements


"Bioinformatics is more about biology and code. It's shells and sessions exports and environments. Ever been confused by login shell vs interactive shell This thread is for you. 🧵"  
[X Link](https://x.com/tangming2005/status/1977732318849896816)  2025-10-13T13:45Z 41.2K followers, [----] engagements


"1/ Whats a login shell Its the shell that starts when you log in via SSH a virtual console or a terminal emulator set to launch a login shell. You'll see it in ps as -bash (the hyphen means login shell). It sets up your environment"  
[X Link](https://x.com/tangming2005/status/1977732330879164483)  2025-10-13T13:45Z 41.2K followers, [--] engagements


"2/ Whats an interactive shell A shell that reads and writes directly from a users terminal. Youre typing into it. You start one by typing: bash Or just open a new terminal tab"  
[X Link](https://x.com/tangming2005/status/1977732342757425255)  2025-10-13T13:45Z 41.2K followers, [--] engagements


"6/ Running a job on an HPC cluster SLURM calls a non-interactive non-login shell by default. Which means: Your PATH PYTHONPATH R_LIBS_USER Might not be loaded unless explicitly sourced"  
[X Link](https://x.com/tangming2005/status/1977732389624520892)  2025-10-13T13:45Z 41.2K followers, [--] engagements


"7/ Example: Your .bash_profile loads conda: source /miniconda3/etc/profile.d/conda.sh But your job crashes with command not found. Why Because your script was run by a non-login shell"  
[X Link](https://x.com/tangming2005/status/1977732401527931116)  2025-10-13T13:45Z 41.2K followers, [--] engagements


"9/ Another tip: Use env or printenv to check your environment. Use ps -f to see if you're in a login shell (-bash). Test before you submit a 3-day job that fails in [--] seconds"  
[X Link](https://x.com/tangming2005/status/1977732425154548094)  2025-10-13T13:45Z 41.2K followers, [--] engagements


"10/ Key takeaways: Login shell sets up your login environment Interactive shell is for live terminal use Non-login non-interactive is how jobs run Always source configs in scripts Know your shell to debug faster Learn your shell. Your scripts will thank you"  
[X Link](https://x.com/tangming2005/status/1977732437141811528)  2025-10-13T13:45Z 41.2K followers, [---] engagements


"Investigating whether deep learning models for co-folding learn the physics of protein-ligand interactions https://www.nature.com/articles/s41467-025-63947-5 https://www.nature.com/articles/s41467-025-63947-5"  
[X Link](https://x.com/tangming2005/status/1977739877908414811)  2025-10-13T14:15Z 41.2K followers, [----] engagements


"Code without structure is like a freezer full of unlabelled tubes. Sure it runs. But good luck figuring out what anything does"  
[X Link](https://x.com/tangming2005/status/1978449581278216348)  2025-10-15T13:15Z 41.2K followers, [--] engagements


"3/ Bad practices hurt you the most. Even if you wrote the code. You: Ill remember this later. Also you (6 weeks later): Who wrote this garbage Still you"  
[X Link](https://x.com/tangming2005/status/1978449592929939572)  2025-10-15T13:15Z 41.2K followers, [--] engagements


"ln -fs /src/FastQC/fastqc /bin/fastqc a symbolic link #ngs2014"  
[X Link](https://x.com/tangming2005/status/496754258898071553)  2014-08-05T20:26Z 40.8K followers, [--] engagements

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