just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at wizardzines.com#posters

Pondering k-Nearest Neighbor density estimation. There's some subtlety making the density smooth and integrate to 1. Here is a simple scheme: - Assign each point a radius from the distance to its kth nearest neighbor. - The density is the sum of a set of Gaussian splats with those radii.

"... a fundamental question that often remains overlooked is whether or not model parameters can be confidently estimated from the available data."

Heatmap in ggplot2 yunuuuu.github.io/ggalign/ind... I always use complexheatmap, but this seems to be a good alternative if you want to stay within the ggplot

Happened to pick up "The Lancet Handbook of Essential Concepts in Clinical Research" (Schulz and Graves). A short read and surprisingly excellent. You can really tell that the authors have seen it all. www.elsevierhealth.com.au/essential-co...

uvx demakein I've finally updated my wind instrument design program to Python 3. It only took me 10 years to get around to. I was pleased to find there is now a fairly solid python library for 3D boolean operations (manifold3d). github.com/pfh/demakein

grug brain bioinformatician not trust maximum a posteriori estimate. big brained bioinformatics shaman develop map estimate. danger! noise demon hide deeper in data! grug prefer count matrix. grug know what to do when have count matrix.

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

🚨 Exciting PhD Opportunities with MACSYS! The MACSYS team at Monash University is offering multiple fully funded #PhD scholarships for students eager to explore the cutting edge of computational biology, microbiology, and systems modelling. 👉More info/apply: macsys.org/monash-phd-s...

👩‍💻 We’re hiring! Lê Cao Lab at Uni Melbourne @mig-unimelb.bsky.social needs an R dev to power the next-gen of mixOmics 🚀 Love #RStats, #Bioconductor & multi-omics? Help expand mixOmics, run workshops & publish cutting-edge methods. Apply: unimelb.wd105.myworkdayjobs.com/en-US/UoM_Ex...

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬 You’d join a welcoming, supportive, and brilliant team. Why not spend a few years in Melbourne and be part of something exciting? Apply here: www.seek.com.au/job/84737876 #ScienceCareers #PostDoc #Bioinformatics

I continue to be astounded at the number of compositional data analysis packages that will happily report differential abundance of individual species. Did they not understand the concept of compositional data? How is it possible to publish methods with this premise?

Normalization and log transformation of log count data. Pseudocounts, library size adjustment, Centered Log Ratios (CLR), Variance Stabilizing Transformation, and all that. Many variations on a similar task. Here's something I haven't seen done:

Random 2d Turing Machines make interesting patterns. pointersgonewild.com/2012/12/31/t...

An experimental design I've seen this three times in different contexts in the last couple of years. The RNA-Seq DE analysis turns out to be non-obvious: You apply treatment X to one group of subjects and treatment Y to another group. You have samples from before and after the treatment.

🧵 PCA is everywhere in bioinformatics—but did you know it’s just SVD in disguise? 1/ If you've done bioinformatics, you've likely used PCA. But did you know Singular Value Decomposition (SVD) is at its core? Let’s break it down. 👇

Happy little accidents...

I'm really liking this course on generative diffusion models. They seem to have boiled many years of confusing development of ideas down to a simple approach. diffusion.csail.mit.edu

Monash University is considering the use of AI assisted assessment. Implementation planned to begin in semester 2 of this year. www.monash.edu/learning-tea...

Comparison of optimization and sampling from a distribution defined by an energy function. I use a continuous version of the Ising model spin lattice energy. First, optimization from a random initial state using gradient descent with momentum, using the SGD optimizer in PyTorch.

I think I'm a little bit in love with the withr package in R. Similar to "with" in Python, you can guarantee to properly clean up when using a resource such as a connection to a file, a temporary directory, or a temporary global setting change. withr.r-lib.org

Bash Strict Mode: Stop Silent Failures in Your Scripts 🧵 1/ Ever had a Bash script fail silently, leading to hours of debugging? Bash doesn't fail by default—it keeps running even after errors. Here's how to fix it with strict mode. 👇

I've been playing with a Langevin Dynamics sampler as an optimizer in PyTorch -- SGD with momentum and noise. It's a remarkably simple algorithm for sampling from a distribution (approximately). Should eliminate over-fitting, and can also be used for generative tasks.

Trying to bring some old family photos back to life with g.i.m.p and its truly amazing resynthesizer add-on created by @paulfharrison.bsky.social getting some pretty good results. Takes me a few hours per photo, but is super satisfying…

This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper: arxiv.org/abs/2412.20509 We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data

If I were to do some virtual half-day workshops this year, what topics and depths might be useful?

I've been watching the 2023 Statistical Rethinking lecture series by Richard McElreath. These cover a complete approach to statistics based on causal reasoning and Bayesian analysis. They are excellent, highly recommend. www.youtube.com/playlist?lis...

10/ TL;DR: ✔️ Under the null, p-values are uniform (flat distribution). ✔️ A "spike near 0" suggests true effects. ✔️ A "U-shape" signals artifacts—time to troubleshoot. Plot your p-values. They’ll tell you more than you think! Have questions? Let’s chat 👇

☎️ calling #SingleCell researchers in 🇦🇺! Join our last community meeting for the year Hear from @lgmartelotto.bsky.social and @swbioinf.bsky.social and chat all things single cell or #SpatialOmics! www.biocommons.org.au/events/sc-sp... #bioinformatics #lifescience

Some years ago I wrote some code that produced a bad plot. I then had to endure multiple people having to explain my bad plot in seminars.

Starting today, The Carpentries will be active on BlueSky! 🥳 We'll continue to maintain our Mastodon (hachyderm.io/@thecarpentr...) and our LinkedIn (www.linkedin.com/company/the-...) accounts, and the content we post on here will be the same as the content we post on Mastodon. Excited to be here!

I just ran my 1.5 hour HTML+SVG+JavaScript+D3 workshop at ResBaz Victoria 2024. Touched on hopefully most of the important ideas needed for an interactive web-based data visualization. #resbaz #resbazvic #resbazvic2024 pfh.github.io/jsfoot/

Our paper "A Plot is Worth a Thousand Tests: Assessing Residual Diagnostics with the Lineup Protocol" has appeared in issue 3 of JCGS, www.tandfonline.com/doi/full/10.... . It is open access for now, but if you ever have problems accessing you'll find the preprint at doi.org/10.48550/arX...

I've begun a statistical graphics starter pack at go.bsky.app/EMb8xWf . Please help me find more people or feeds to add to this pack. #rstats #visualisation #statistics 📈

Great 'cos I just started this one. go.bsky.app/NmhwfbN

Pondering FDR control. Procedures like BH represent a certain policy, which can be confirmed to work by simulation for any given number of true discoveries. The actually achieved FDR guarantee is the FDR obtained in the worst case.

Our collaborative work with Narry Kim on the kinetics of mRNA poly(A) tail shortening. Led by Young-suk Lee, who established his own lab while the work was in progress, and Yevgen Levdansky in my lab. #RNASky #RNABiology www.nature.com/articles/s41...

Something that should exist: geom_principal_curve() If x and y have a symmetric relationship, eg both x and y are noisy measurements of an underlying hidden variable, geom_smooth will under-estimate the slope, just like linear regression.

sgdGMF is a general purpose matrix factorization package. Like PCA, but better, e.g. works well with count data. Should be fast, e.g. suitable for scRNA-Seq. Presented by @davi1893.bsky.social at #abacbs2024. github.com/CristianCast...

The Knockoff Framework looks very interesting as a broadly applicable method of maintaining an FDR. (Guannan Yang talked about this at #abacbs2024) web.stanford.edu/group/candes...

Jingyi Jessica Li demonstrates how to use permutations to test the accuracy of tSNE and UMAP #ABACBS2024

A nice video on power calculation by simulation. www.youtube.com/watch?v=vE8b...

Registrations for ResBas Victoria 2024 at Monash University are now open. The program is looking quite varied, it's going to be an adventure! #resbaz #resbazvic2024 resbaz.github.io/resbazvic202...

New CRAN Task View: Dynamic Visualizations and Interactive Graphics #rstats #dataviz By Sherry Zhang, Dianne Cook @visnut.bsky.social URL: cran.r-project.org/view=Dynamic...

High FDR rates from edgeR and DESeq2 for large datasets, seems a little concerning. I have noticed edgeR has a tendency to call genes differentially expressed on the basis of a single sample with high expression (have not tried with latest version). genomebiology.biomedcentral.com/articles/10....

This week the Monash Genomics and Bioinformatics Platform did a bulk RNA-Seq workshop, covering end-to-end from experimental design, through library preparations, running an analysis pipeline, and digging into differential expression.

We'll be hosting a set of tutorials and workshop in Melbourne, Oct 22-23, on the theme "Open the World with Open Source". Details can be found at wombat2024.numbat.space. Registration opens today. Hope you can join us!

Nice illustrations of methods to learn energy landscapes. mpmisko.github.io/2024/ai-fund...

Running something with an HTTP interface on a remote machine? Here's a port forwarding command good for a laptop. Unlike "ssh -L ...", the listening socket survives sleeping, change of network. socat TCP4-LISTEN:1234,fork,bind=127.0.0.1 EXEC:'"ssh my.remote.server socat - TCP4:127.0.0.1:1234"'

Ok, parquet is cool. parquet is a format for tabular data. Data is stored in row-blocks, and then compressed column-wise within row-blocks. Row blocks also have metadata for min and max values of columns.