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alabaster.sfe

Language agnostic on disk representation of SFE objects

https://github.com/pachterlab/alabaster.sfe

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 2 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Language agnostic on disk representation of SFE objects

Basic Info
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 2
  • Open Issues: 2
  • Releases: 0
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

alabaster.sfe

Codecov test coverage R-CMD-check <!-- badges: end -->

The goal of alabaster.sfe is to implement a language agnostic format to represent SpatialFeatureExperiment on disk, as in the existing alabaster packages from ArtifactDB. This serves to formalize and standardize the files written to disk when SFE reformats smFISH transcript spots and to improve interoperability between the R and Python implementations of Voyager.

Installation

You can install the development version of alabaster.sfe from GitHub with:

``` r

install.packages("devtools")

devtools::install_github("pachterlab/alabaster.sfe") ```

This package has been submitted to Bioconductor and is under review

Owner

  • Name: Pachter Lab
  • Login: pachterlab
  • Kind: organization
  • Email: lpachter@caltech.edu
  • Location: Pasadena, CA

GitHub Events

Total
  • Issues event: 4
  • Issue comment event: 1
  • Public event: 1
  • Push event: 39
  • Pull request event: 4
  • Fork event: 2
  • Create event: 1
Last Year
  • Issues event: 4
  • Issue comment event: 1
  • Public event: 1
  • Push event: 39
  • Pull request event: 4
  • Fork event: 2
  • Create event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 21
  • Total Committers: 2
  • Avg Commits per committer: 10.5
  • Development Distribution Score (DDS): 0.048
Past Year
  • Commits: 19
  • Committers: 2
  • Avg Commits per committer: 9.5
  • Development Distribution Score (DDS): 0.053
Top Committers
Name Email Commits
Lambda Moses d****2@c****u 20
vjcitn s****c@c****u 1
Committer Domains (Top 20 + Academic)
channing.harvard.edu: 1 caltech.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 3
  • Total pull requests: 3
  • Average time to close issues: about 23 hours
  • Average time to close pull requests: 3 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: about 23 hours
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jkanche (1)
  • lambdamoses (1)
  • alikhuseynov (1)
Pull Request Authors
  • vjcitn (2)
  • alikhuseynov (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 984 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
bioconductor.org: alabaster.sfe

Language agnostic on disk serialization of SpatialFeatureExperiment

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 984 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 30.3%
Average: 41.1%
Downloads: 92.9%
Maintainers (1)
dl3764@columbia.edu
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • codecov/codecov-action v4 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • SpatialFeatureExperiment >= 1.9.3 depends
  • alabaster.base * depends
  • EBImage * imports
  • RBioFormats * imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • alabaster.sce * imports
  • alabaster.spatial >= 1.5.2 imports
  • jsonlite * imports
  • methods * imports
  • sfarrow * imports
  • spdep * imports
  • terra * imports
  • xml2 * imports
  • BiocStyle * suggests
  • SFEData * suggests
  • Voyager >= 1.9.1 suggests
  • fs * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • scater * suggests
  • sf * suggests
  • testthat >= 3.0.0 suggests