Sainsc.jl

Sainsc.jl - Segmentation-free analysis of in situ capture data^[1] - is, as the name states, a tool to analyse in situ capture-based spatial transcriptomics data. Actually, it can also be used to analyse imaging-based datasets. For a more thorough background please refer to the original publication. or just follow along the provided examplary analysis.

A more batteries included^[2] version of this package is available in Python/Rust. If you are interested have a look at https://github.com/HiDiHlabs/sainsc.

Citation

If you are using Sainsc.jl for your research please consider citing

Müller-Bötticher, N., Tiesmeyer, S., Eils, R., and Ishaque, N. "Sainsc: a computational tool for segmentation-free analysis of in-situ capture" bioRxiv (2024) https://doi.org/10.1101/2024.08.02.603879

Installation

The package can be installed with the Julia package manager. From the Julia REPL, type ] to enter the Pkg REPL mode and run:

pkg> add Sainsc

Or, alternatively, via the Pkg API:

using Pkg
Pkg.add("Sainsc")

Index

• Example analysis
• • General workflow
  • • Loading data
    • Kernel
    • Local Maxima
    • Cell-type map
  • Utils
  • • Cropping & Masking
    • Binning
• Reference API
• • Index
  • API