https://github.com/kstreet13/slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
https://github.com/kstreet13/slingshot

Last synced: 23 days ago
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Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

• Host: GitHub
• URL: https://github.com/kstreet13/slingshot
• Owner: kstreet13
• Created: 2016-03-11T18:43:06.000Z (over 8 years ago)
• Default Branch: main
• Last Pushed: 2024-04-23T23:33:24.000Z (2 months ago)
• Last Synced: 2024-04-24T00:26:22.575Z (2 months ago)
• Language: R
• Homepage:
• Size: 260 MB
• Stars: 245
• Watchers: 7
• Forks: 41
• Open Issues: 7
• Metadata Files:
  • Readme: README.md

Lists

• awesome_single_cell - slingshot - [R] - Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data. (Software packages / RNA-seq)
• awesome-single-cell - slingshot - [R] - Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data. (Software packages / Pseudotime and trajectory inference)
• awesome-single-cell - slingshot - [R] - Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data. (Software packages / RNA-seq)
• roryk-awesome-single-cell - slingshot - [R] - Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data. (Software packages)

README

        
# R package: slingshot

[![R build status](https://github.com/kstreet13/slingshot/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/kstreet13/slingshot/actions)

[![Coverage Status](https://img.shields.io/codecov/c/github/kstreet13/slingshot/master.svg)](https://codecov.io/github/kstreet13/slingshot?branch=master)



Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

## Installation

```r

if (!requireNamespace("BiocManager", quietly=TRUE))

    install.packages("BiocManager")

BiocManager::install("kstreet13/slingshot")

```

## Python Version

An implementation of the Slingshot algorithm in `python` can be found here: https://github.com/mossjacob/pyslingshot

## Issues and bug reports

Please use https://github.com/kstreet13/slingshot/issues to submit issues, bug reports, and comments.