Coder Social home page Coder Social logo

scmasigpro's Introduction

scMaSigPro Logo

Implementation of MaSigPro for scRNA-Seq Data.

R-CMD-Check test-coverage


Introduction

scMaSigPro is an R package designed for analyzing single-cell RNA-seq data over pseudotime. Building on the maSigPro package, it identifies genes with significant expression changes across branching paths in a pseudotime-ordered dataset. This guide provides a step-by-step workflow for ScMaSigPro, making it accessible for users.

Installation

To install scMaSigPro from GitHub, use the following R code:

# Install devtools if not already installed
if (!requireNamespace("devtools", quietly = TRUE)) {
    install.packages("devtools")
}

# Install scMaSigPro
devtools::install_github("BioBam/scMaSigPro",
                         ref = "main",
                         build_vignettes = FALSE,
                         build_manual = TRUE,
                         upgrade = "never",
                         force = TRUE,
                         quiet = TRUE)

Basic Usage

The basic workflow of scMaSigPro involves the following steps:

1. Load Package and Dataset

set.seed(123)
library(scMaSigPro)
data("splat.sim", package = "scMaSigPro")

2. Create scMaSigPro Object

# Helper Function to convert annotated SCE object to scmpObject
scmp.ob <- as_scmp(
  object = splat.sim, from = "sce",
  align_pseudotime = FALSE,
  verbose = TRUE,
  additional_params = list(
    labels_exist = TRUE,
    exist_ptime_col = "Step",
    exist_path_col = "Group"
  )
)

3. Pseudo-bulking with sc.squeeze()

This function discretizes a continuous pseudotime column into bins:

scmp.ob <- sc.squeeze(scmp.ob)

4. Setting up the Polynomial Model

scmp.ob <- sc.set.poly(scmp.ob)

5. Detecting Genes with Non-Flat Profiles

scmp.ob <- sc.p.vector(scmp.ob)

6. Model Refinement

scmp.ob <- sc.t.fit(scmp.ob)

7. Gene selection with $R^2$

scmp.ob <- sc.filter(scmp.ob, vars = "all")

8. Gene Trend Visualization

plotTrend(scmp.ob, "Gene10")

For detailed instructions and additional steps, please refer to the following vignettes.

Contributing

Contributions, including bug reports, suggestions, and pull requests, are welcome.

License

This project is licensed under GPL>=2 - see the LICENSE.md file for details.

Funding Information

This project has received funding from the European Union’s Framework Programme for Research and Innovation Horizon 2020 (2014-2020) under the Marie Skłodowska-Curie Grant Agreement No 953407.

Citation

If you use scMaSigPro in your research, please cite:


scmasigpro's People

Contributors

spriyansh avatar martabenegas avatar

Watchers

Stefan Götz avatar Robert Nica avatar  avatar

Forkers

spriyansh

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.