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const-ae.bsky.social
Postdoc at UCL with James Reading. Previously at EMBL working with Wolfgang Huber. Biostats, R, cancer immunology
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Is there some clever syntax to control when a quasi-quotation is evaluated so that the wrap_in_tibble function works? 🧐 (Context in stackoverflow.com/questions/79...) #Rstats #rlang

Thrilled to share that our work from Trumpp Lab @hi-stem @dkfz.bsky.social is out in Nature. We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social www.nature.com/articles/s41...

I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... πŸŽ‰ It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility. #rstats

@epigenci.bsky.social makes a pretty convincing case for pseudobulk (as opposed to GLMMs) in multi-sample single cell studies here: doi.org/10.1093/bioi... . #bioinformatics

We have additional available spots. Please consider joining! It will be a blast.

CSAMA 2025 Biological Data Science Summer School in Brixen, South Tyrol, 7-11 July We cover (sc)-RNA-seq and spatial omics data analysis, underlying (bio)statistical topics, multi-omics, ... All hands-on using R/Bioconductor tools. csama2025.bioconductor.eu Registration opens on 1 Feb

My first post here on BlueSky to share our recent work with Claudia Feng and @leopoldparts.bsky.social - a large-scale single cell CRISPR screen to chart out gene regulation and the role of genomic background in iPSCs. Check out the data here: www.sanger.ac.uk/tool/crispri...

Come do a PhD with me! πŸ–₯️🧬 We've got very exciting multiomics data coming in, you get to shape the project and there are lots of opportunities to collaborate and learn. Reach out here or via email if you have questions Please reskeet πŸ™ www.werkenbijerasmusmc.nl/en/vacancy/1...

For the Monday morning crowds :) Also take a look at my blog post where I compress the full lemur package into 100 lines of code and explain the core algorithm. const-ae.name/post/2025-01...

After 4y in the making, I am super excited that my main PhD project is published πŸŽ‰πŸ₯³πŸŽ‰πŸŽ‰πŸ₯³ www.nature.com/articles/s41... LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️

PSA for authors posting to bioRxiv, who don't want to miss if someone comments on their preprint or writes a review: Click "follow" on your papers! Otherwise, you won't be notified. βœ‰οΈπŸš¨

@richardsever.bsky.social, is there a setting as an author on bioRxiv to be notified if someone posts a comment about one of my preprints? Or maybe get a notification from prereview.bsky.social? I received a comment in November and only saw it today!

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/

I wrote a new blogpost about working with D3 (or any other Javascript library) from R. Existing wrappers, like R2D3, where last updated in 2021. But with a few (low-level) function calls we can load any JS library and even send data from R to JS! const-ae.name/post/2024-12... #rstats

Extremely proud to see my PhD project exploring intra-tumor heterogeneity in complex karyotype AML finally out in @NatureGenet! πŸŽ‰ πŸ‘©πŸ»β€πŸ”¬ They say that 10,000 hours make you an expert, so I guess after more than five years of work I’m half-way there πŸ˜… ⬇️1/5 www.nature.com/articles/s41...

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics) go.bsky.app/TRWCnZs

πŸ«£πŸ‘€ Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods https://www.biorxiv.org/content/10.1101/2024.09.16.613342v1

There's a lot of excitement about foundation models and their ability to learn biology πŸ§¬πŸ’» But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress. www.biorxiv.org/content/10.1...

Very excited to announce that I started a postdoc in James Reading's lab at UCL working on tumor immunology πŸ₯³ So, if you are in London and want to meet for a coffee, hit me up :)

Over on mastodon, @teunbrand.bsky.social presented his new package {{gguidance}} to customize your legends and axis in #ggplot: fosstodon.org/@teunbrand/1... Now you can, for example, easily distinguish groups of discrete labels without facetting! #rstats

Great conference with lots of exciting science! πŸ§ͺπŸ§¬πŸ’»

I wrote a new ggplot2 extension to draw Bezier curves github.com/const-ae/ggb... πŸŽ‰ The curves are defined by a set of control points and the tangents at those points. This makes each parameter directly interpretable and easy to tweak! #rstats #ggplot2

Job at EMBL Heidelberg: Bioinformatician Scientific Data Manager and Research Software Engineer in Precision Oncology and Multiomics www.embl.org/jobs/positio...

I recently had to convert a manuscript written in Latex to Word and pandoc made the process mostly straightforward. In this blog post, I describe how I fixed some of the remaining edge cases :) const-ae.name/post/2024-08...

Over at Twitter, my colleague Paula has posted about our new R package {{fullRankMatrix}} available on CRAN twitter.com/PaulaH_W/sta... Check it out at github.com/Pweidemuelle... The package helps with design matrices that contain colinear columns. #rstats

Excited to announce pyLemur, a Python version of LEMUR pylemur.readthedocs.io/en/latest/no... Just run `pip install pyLemur` and predict diff. expr. without clusters! πŸ₯³ 🧬 πŸ–₯️ To learn more about LEMUR, check out my talk at the scverse-meeting from last month: youtu.be/cBkjJLoLX-g?...

Open Position: Scientific Lab and Project Manager at EMBL Heidelberg www.embl.org/jobs/positio...

Join me in 1.5h at the scverse community call (connection details at scverse.zulipchat.com#narrow/strea... ) to learn about LEMUR, differential geometry for single-cell, and get a sneak peek of an upcoming Python package! pylemur.readthedocs.io/en/latest/in...

Had a lot of fun teaching horizontal data integration at the EMBO multi-omics course! We went over strategies to neutralize batch effects and account for conditions in single-cell data. 🧬 πŸ–₯️ You can find my tutorial at htmlpreview.github.io?https://gith...