https://github.com/biojulia/singlecellprojections.jl

Analysis of Single Cell Expression data in Julia
https://github.com/biojulia/singlecellprojections.jl

Last synced: about 1 year ago
JSON representation

Analysis of Single Cell Expression data in Julia

• Host: GitHub
• URL: https://github.com/biojulia/singlecellprojections.jl
• Owner: BioJulia
• License: other
• Created: 2023-01-15T08:22:38.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2025-03-27T16:20:18.000Z (about 1 year ago)
• Last Synced: 2025-04-11T13:46:27.976Z (about 1 year ago)
• Language: Julia
• Size: 1.37 MB
• Stars: 19
• Watchers: 3
• Forks: 3
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# SingleCellProjections.jl

[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.dev/SingleCellProjections.jl/stable/)

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.dev/SingleCellProjections.jl/dev/)

[![Build Status](https://github.com/BioJulia/SingleCellProjections.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/BioJulia/SingleCellProjections.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/BioJulia/SingleCellProjections.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/BioJulia/SingleCellProjections.jl)

SingleCellProjections.jl is an easy to use and powerful package for analysis of Single Cell Expression data in Julia.

It is faster and uses less memory than existing solutions since the data is internally represented as expressions of sparse and low rank matrices, instead of storing huge dense matrices.

In particular, it efficiently performs PCA (Principal Component Analysis), a natural starting point for downstream analysis, and supports both standard workflows and projections onto a base data set.

## Installation

Install SingleCellProjections.jl by running the following commands in Julia:

```julia

using Pkg

Pkg.add("SingleCellProjections")

```

## Threading

SingleCellProjections.jl relies heavily on threading. Please make sure to [enable threading in Julia](https://docs.julialang.org/en/v1/manual/multi-threading/) to dramatically improve computation speed.

## Tutorial

Here is a [tutorial](https://biojulia.dev/SingleCellProjections.jl/dev/tutorial/), showcasing SingleCellProjections.jl functionality using a PBMC (Peripheral Blood Mononuclear Cell) data set.

![force_layout](https://user-images.githubusercontent.com/16546530/228492990-14c31888-28e1-4f3c-8062-f10682e55430.svg)

Force layout plot of the PBMC data.

## Documentation

For more information, please refer to the [documentation](https://biojulia.dev/SingleCellProjections.jl/dev/).