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slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

https://github.com/kstreet13/slingshot

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 13 committers (30.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor bioinformatics single-cell transcriptomics genomics scrna-seq gene core-services gene-expression
Last synced: 11 months ago · JSON representation

Repository

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

Basic Info
  • Host: GitHub
  • Owner: kstreet13
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 260 MB
Statistics
  • Stars: 287
  • Watchers: 8
  • Forks: 44
  • Open Issues: 4
  • Releases: 0
Created over 10 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog

README.md

R package: slingshot

R build status Coverage Status

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.

Owner

  • Name: Kelly Street
  • Login: kstreet13
  • Kind: user
  • Location: Los Angeles, CA
  • Company: Keck School of Medicine of USC

Assistant Professor of Population and Public Health Sciences, Division of Biostatistics

GitHub Events

Total
  • Issues event: 17
  • Watch event: 31
  • Issue comment event: 12
  • Fork event: 5
Last Year
  • Issues event: 17
  • Watch event: 31
  • Issue comment event: 12
  • Fork event: 5

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 507
  • Total Committers: 13
  • Avg Commits per committer: 39.0
  • Development Distribution Score (DDS): 0.462
Past Year
  • Commits: 6
  • Committers: 2
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Kelly Street k****t@b****u 273
Kelly Street k****t@r****l 80
Kelly Street k****t@r****u 66
Robrecht Cannoodt r****d@g****m 25
Kelly Street s****y@g****m 15
Robrecht Cannoodt b****s@g****m 15
Nitesh Turaga n****a@g****m 14
Robrecht Cannoodt r****t@u****e 12
J Wokaty j****y@s****u 2
vobencha v****a@g****m 2
Hector Roux de Bézieux h****x@b****u 1
LiNk-NY m****9@g****m 1
Peter Hickey p****y@g****m 1
Committer Domains (Top 20 + Academic)
berkeley.edu: 2 sph.cuny.edu: 1 ugent.be: 1 root-pcs-air.dfci.harvard.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 15
  • Total pull requests: 0
  • Average time to close issues: 10 months
  • Average time to close pull requests: N/A
  • Total issue authors: 14
  • Total pull request authors: 0
  • Average comments per issue: 1.87
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 0
  • Average time to close issues: 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 7
  • Pull request authors: 0
  • Average comments per issue: 0.57
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Yanst86 (2)
  • TdzBAS (2)
  • handesome (2)
  • ayyildizd (1)
  • HappinessEricst (1)
  • Dazcam (1)
  • HelenaLC (1)
  • Leoarie-lab (1)
  • erzakiev (1)
  • Capiques (1)
  • pariaaliour (1)
  • royfrancis (1)
  • benwinog (1)
  • RunyuXia (1)
  • Saumya513 (1)
Pull Request Authors
  • Angle28 (1)
  • TongzhenXu (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • TrajectoryUtils * depends
  • princurve >= 2.0.4 depends
  • stats * depends
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • grDevices * imports
  • graphics * imports
  • igraph * imports
  • matrixStats * imports
  • methods * imports
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • DelayedMatrixStats * suggests
  • RColorBrewer * suggests
  • clusterExperiment * suggests
  • covr * suggests
  • knitr * suggests
  • mclust * suggests
  • mgcv * suggests
  • rgl * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • uwot * suggests
.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite