Introducing me and my first Julia package SiCell.jl

Specific Domains Biology, Health, and Medicine
1

Hi everyone :waving_hand:

My name is Masoud, and I’m excited to finally share my first Julia package with the community: SiCell.jl.

SiCell is a high-performance single-cell RNA-seq toolkit I’ve been working on for the past several months. After getting tired of waiting for R and Python to finish basic operations on large datasets, I decided to build something faster in Julia :slight_smile:

The main feature I’m most proud of is TUF (Trajectory Uncertainty Framework) — a new approach that introduces two metrics:

  • TES (Temporal Entropy Score) — detects cells in transitional or ambiguous transcriptional states
  • TDS (Trajectory Divergence Score) — identifies potential branching points and decision moments

Together, they aim to go beyond traditional pseudotime and better capture cellular plasticity and uncertainty in developmental trajectories.

What’s included:

  • Full scRNA-seq pipeline (QC, normalization, clustering, UMAP, diffusion maps, pseudotime)
  • The TUF uncertainty metrics (TES + TDS)
  • Focus on performance and ease of use

Repo: GitHub - Sizerta/SiCell.jl · GitHub

Since this is my first Julia package, I’d really appreciate any feedback — whether it’s about the API, documentation, performance, or potential improvements. I’m also very open to collaborators or early testers, especially people working with developmental or branching systems.

Looking forward to your thoughts and suggestions! :folded_hands:

Thank you!

2

Hi Masoud,

Welcome! :waving_hand: Apologies for the delay in commenting - summer was a bit of a whirlwind!

I’m curious if you’ve seen @rasmushenningsson 's work SingleCellProjections.jl? We’ve also been wanting an RNAseq tutorial for biojulia (here is one such effort that’s not quite done - if you’re interested in contributing to BioJulia we’d be happy to get your oriented.

Cheers!
Kevin

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The cases study in the doc are cool, although I’m not a single cell expert. I’d remove some of the emoji’s from the readme/docs since that gives a slop impression.

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Thanks. I’ll correct that. I thought biologists would like it because it’s designed for them, but it turns out I may have overdone it a little.

5

Hi Kevin,

Thanks for the welcome, and no worries at all. I hope you had a good summer.

Yes, I’ve seen SingleCellProjections.jl, and it’s great to see related work in the BioJulia Ecosystem. I’ll take a closer look at it to see how it relates to SiCell.jl.

I’d also be interested in contributing to the BioJulia.
Best regards.

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Hi Masoud, this looks cool, I’ll check it out when I get some time!
In the meantime, just want to make sure you’re aware of GitHub - scverse/Muon.jl: Muon for Julia · GitHub (MuData / AnnData implementation from the scverse folks)

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That is awesome! Congrats and welcome

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Thank you. Yes, I’m aware of Muon.jl. For SiCell’s I/O, I actually treated it a bit like a challenge to use as few Julia libraries as I can and implement the handling myself. It was a really fun and instructive experience, especially getting into the details of the different formats and their edge cases.

I’ll definitely keep Muon.jl in mind as I continue developing SiCell and thinking about interoperability.