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ggspavis

Visualization functions for spatial transcriptomics data in R

https://github.com/lmweber/ggspavis

Science Score: 39.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Visualization functions for spatial transcriptomics data in R

Basic Info
  • Host: GitHub
  • Owner: lmweber
  • License: mit
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 376 KB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Created over 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

ggspavis

R build status

The ggspavis package contains visualization functions for spatial transcriptomics data, including functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment Bioconductor format.

The package is available from Bioconductor.

Installation

The release version of the package can be installed from Bioconductor:

install.packages("BiocManager") BiocManager::install("ggspavis")

The latest development version can be installed either from the development version of Bioconductor or from GitHub:

remotes::install_github("lmweber/ggspavis")

Tutorial

A vignette containing a tutorial and examples is available from the Bioconductor package page.

Citation

  • Righell D.*, Weber L.M.*, Crowell H.L.*, Pardo B., Collado-Torres L., Ghazanfar S., Lun A.T.L., Hicks S.C.*, and Risso D.* (2022). SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor. Bioinformatics, btac299.

Owner

  • Name: Lukas Weber
  • Login: lmweber
  • Kind: user
  • Location: Boston, MA
  • Company: Boston University

Assistant Professor, Department of Biostatistics, Boston University

GitHub Events

Total
  • Issues event: 5
  • Watch event: 1
  • Issue comment event: 5
  • Push event: 11
  • Pull request event: 1
  • Create event: 1
Last Year
  • Issues event: 5
  • Watch event: 1
  • Issue comment event: 5
  • Push event: 11
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 128
  • Total Committers: 3
  • Avg Commits per committer: 42.667
  • Development Distribution Score (DDS): 0.039
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lukas Weber l****u@g****m 123
Nitesh Turaga n****a@g****m 4
HelenaLC h****a@c****u 1
Committer Domains (Top 20 + Academic)
crowells.eu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 13
  • Total pull requests: 6
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 5 months
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 1.54
  • Average comments per pull request: 1.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 25 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • boyiguo1 (4)
  • nilseling (2)
  • lmweber (2)
  • giovp (2)
  • estellad (1)
  • csoneson (1)
  • HelenaLC (1)
Pull Request Authors
  • estellad (5)
  • boyiguo1 (2)
  • HelenaLC (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 12,308 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 1
bioconductor.org: ggspavis

Visualization functions for spatial transcriptomics data

  • Versions: 9
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 12,308 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 27.5%
Downloads: 82.4%
Maintainers (1)
lmweberedu@gmail.com
Last synced: 11 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
DESCRIPTION cran
  • ggplot2 * depends
  • SingleCellExperiment * imports
  • SpatialExperiment * imports
  • SummarizedExperiment * imports
  • ggside * imports
  • grid * imports
  • methods * imports
  • stats * imports
  • BiocStyle * suggests
  • BumpyMatrix * suggests
  • STexampleData * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • scater * suggests
  • scran * suggests
  • testthat >= 3.0.0 suggests
  • uwot * suggests