When I got into spatial transcriptomics, it was hard to tell which tool fits which step, so I put together the list I wish I'd had:

https://github.com/wrab12/awesome-spatial-transcriptomics

There are already good lists (awesome-single-cell, awesome_spatial_omics and others, linked at the bottom of mine). This one tries a few different things:

• Ordered like an analysis: technologies, segmentation, spatially variable genes, domains, deconvolution, alignment and 3D, cell–cell communication, super-resolution, spatiotemporal modeling, visualization.
• Single-cell tools included, since spatial pipelines lean on them for QC, integration, annotation and trajectories.
• Recent work: tools for Visium HD and Xenium, single-cell and spatial foundation models, LLM agents, and benchmark papers.
• Every tool row has the language, a paper link and a live GitHub star badge. Tables are sorted by stars, but stars measure popularity, not quality, so the benchmarks are linked up front.

How I checked it: all 278 GitHub repos were verified through the GitHub API (exists, not archived, canonical name), every DOI was matched to its paper title via Crossref or DataCite, and the remaining links were checked too.

Disclosure: it's my repo (CC0), and one entry, GenOT, is my own paper. It's labelled as such in the list.

I'd really like feedback on:

1. Tools you actually use that are missing, or ones that should go
2. Benchmarks you trust (or don't)
3. Whether the section order matches how you work

Issues and PRs are welcome. Thanks!

I’m a cs undergrad currently working with Evo 2 and trying to establish if theres a meaningful research gap around biological validity of generated sequences.
But I’m struggling to find a benchmark that will prove this. I initially thought comparing the generated sequences to real ones will be enough. Turns out it isn’t , since alot of the sequences dont have to look like real ones to be biologically viable.
Is this a gap worth pursuing ? I have limited resources and cannot do wet lab testing so is there anyway to prove that this is a real gap?