Ali Altıntaş
@altintasali.bsky.social
Assistant Professor, University of Copenhagen 🇩🇰 | #Bioinformatician | #Molecular #Biologist | Forged in 🇹🇷
And finally, huge congrats, Bahtiyar Yılmaz! 👏 Thanks for the opportunity and for leading such an impressive piece of work. Proud to be part of this global effort with you! 🌍🧬
November 10, 2025 at 1:48 PM
And finally, huge congrats, Bahtiyar Yılmaz! 👏 Thanks for the opportunity and for leading such an impressive piece of work. Proud to be part of this global effort with you! 🌍🧬
🔍 Want to explore the data yourself? Check out the interactive resources:
🔗 yilmazlab.shinyapps.io/vivaria_app/
🔗 yilmazlab.shinyapps.io/vivaria_app2/
🔗 yilmazlab.shinyapps.io/vivaria_app/
🔗 yilmazlab.shinyapps.io/vivaria_app2/
November 10, 2025 at 1:39 PM
🔍 Want to explore the data yourself? Check out the interactive resources:
🔗 yilmazlab.shinyapps.io/vivaria_app/
🔗 yilmazlab.shinyapps.io/vivaria_app2/
🔗 yilmazlab.shinyapps.io/vivaria_app/
🔗 yilmazlab.shinyapps.io/vivaria_app2/
❓ And what if your species is not present in this database? What do you do then?
❓ Isn't it enough to decide on an arbitrary cutoff (e.g. TPM < 1) for expression?
👉 Actually, you can do better than that. How? #BgeeCall #R package:
www.bioconductor.org/packages/rel...
❓ Isn't it enough to decide on an arbitrary cutoff (e.g. TPM < 1) for expression?
👉 Actually, you can do better than that. How? #BgeeCall #R package:
www.bioconductor.org/packages/rel...
August 26, 2025 at 12:22 PM
❓ And what if your species is not present in this database? What do you do then?
❓ Isn't it enough to decide on an arbitrary cutoff (e.g. TPM < 1) for expression?
👉 Actually, you can do better than that. How? #BgeeCall #R package:
www.bioconductor.org/packages/rel...
❓ Isn't it enough to decide on an arbitrary cutoff (e.g. TPM < 1) for expression?
👉 Actually, you can do better than that. How? #BgeeCall #R package:
www.bioconductor.org/packages/rel...
August 5, 2025 at 12:24 PM
"(...) This is present for the pairs (body_mass_mm, bill_depth_mm) and (bill_depth_mm, bill_length_mm)."
May 28, 2025 at 1:43 PM
"(...) This is present for the pairs (body_mass_mm, bill_depth_mm) and (bill_depth_mm, bill_length_mm)."
From the vignette after I fixed the typos: "Pairs of numeric variables exhibit Simpson's paradox if the ungrouped correlation is negative and the grouped correlations are positive (or vice-versa). (...)"
May 28, 2025 at 1:43 PM
From the vignette after I fixed the typos: "Pairs of numeric variables exhibit Simpson's paradox if the ungrouped correlation is negative and the grouped correlations are positive (or vice-versa). (...)"
🔑 Key takeaway: Check total RNA & RNA composition before comparing RPKM/TPM across samples/protocols to avoid misleading results!
April 7, 2025 at 11:27 AM
🔑 Key takeaway: Check total RNA & RNA composition before comparing RPKM/TPM across samples/protocols to avoid misleading results!
📊 For DEGs, use count-based methods like DESeq2/edgeR, not direct RPKM/TPM.
April 7, 2025 at 11:27 AM
📊 For DEGs, use count-based methods like DESeq2/edgeR, not direct RPKM/TPM.
✅ TPM can be okay for qualitative comparisons (PCA, clustering) under the right conditions.
April 7, 2025 at 11:27 AM
✅ TPM can be okay for qualitative comparisons (PCA, clustering) under the right conditions.
🛑 NEVER use TPM for quantitative comparisons across samples with very different total RNA or distributions!
April 7, 2025 at 11:27 AM
🛑 NEVER use TPM for quantitative comparisons across samples with very different total RNA or distributions!
📉 Abundant RNAs (rRNA, globin, etc.) can inflate their TPM and deflate others.
April 7, 2025 at 11:27 AM
📉 Abundant RNAs (rRNA, globin, etc.) can inflate their TPM and deflate others.
⚠️ Only compare RPKM/TPM if total RNA & RNA populations are similar. This is often not checked!
April 7, 2025 at 11:27 AM
⚠️ Only compare RPKM/TPM if total RNA & RNA populations are similar. This is often not checked!
🧬 Stranded vs. non-stranded RNA-seq impacts results. Comparing TPM/RPKM across these can be wrong.
April 7, 2025 at 11:27 AM
🧬 Stranded vs. non-stranded RNA-seq impacts results. Comparing TPM/RPKM across these can be wrong.
🔬 RNA location (nucleus vs. cytoplasm) matters! Don't directly compare TPMs from different compartments.
April 7, 2025 at 11:27 AM
🔬 RNA location (nucleus vs. cytoplasm) matters! Don't directly compare TPMs from different compartments.
⚠️ Tissue types express diverse RNA repertoires. Direct TPM comparisons across such different tissues are problematic
April 7, 2025 at 11:27 AM
⚠️ Tissue types express diverse RNA repertoires. Direct TPM comparisons across such different tissues are problematic