Bryan Downie

Oh, got it. Yeah, I think it makes sense. Your transcriptome is probably going to be a lot cleaner too, and I'd expect higher N50 (ExN50?) because your graph will have less noise. Makes sense to me!

11.12.2024 21:03 — 👍 1    🔁 0    💬 0    📌 0

I think there's a lot of missing information that is needed to understand this problem better (e.g. library prep?, how are you defining non-eukaryotic RNA? Aligning first to a eukaryotic transcriptome reference db?). But I think it makes sense that your assembly doesn't change much.

11.12.2024 20:14 — 👍 1    🔁 0    💬 1    📌 0

🧪🧬 colleagues, anyone looking to collaborate on a single cell method for robust UMAP clustering and annotation? I've done initial analysis the results look promising and batch-resilient. I need someone(s) who is way deeper in single cell analysis methodology/normalization than I am.

11.12.2024 16:55 — 👍 3    🔁 0    💬 0    📌 0

What's the current state of the art for differential isoform detection using short read sequencing? I see you are providing DEXSeq integration, is that approach still preferable? I've always thought (intuitively) that something like salmon would provide good results.

11.12.2024 02:13 — 👍 0    🔁 0    💬 0    📌 0

It can also be customized pretty easily with an LLM. For example, I just asked ChatGPT to write FASTQ -> counts -> DEG analysis, and it used hisat2. I can then just tell it I wanted salmon or STAR instead and it would adapt.

11.12.2024 02:10 — 👍 1    🔁 0    💬 0    📌 0

I would think they'd be helpful. Most of the way that students learn new analytical workflows is through vignettes or example documentation, and an LLM would have the benefit of being able to explain the individual components as-needed.

11.12.2024 02:08 — 👍 3    🔁 0    💬 2    📌 0

Patients with High Baseline Neutrophil-to-Lymphocyte Ratio Exhibit Better Response to Filgotinib as Treatment for Rheumatoid Arthritis - Rheumatology and Therapy Introduction High baseline neutrophil-to-lymphocyte ratio (NLR) in rheumatoid arthritis (RA) has been associated with positive responses to biologic tumor necrosis factor inhibition and negative respo...

A recent publication I led investigating the predictive value of the #NeutrophilLymphocyteRatio in #RheumatoidArthritis

#PrecisionMedicine #Immunology #ClinicalResearch

09.12.2024 20:18 — 👍 2    🔁 0    💬 0    📌 0

Same, figure 1 is the first thing I look at (usually followed by Figure ~4, which is usually the key experiment that brings everything together)

09.12.2024 20:09 — 👍 1    🔁 0    💬 0    📌 0

One of the first posts on my feed is from @flavorflav.bsky.social . This social network is off to a very auspicious start.

09.12.2024 19:44 — 👍 2    🔁 1    💬 0    📌 0