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SpaceMarkers

An R/Bioconductor software tool to identify genes associated with latent space interactions in spatial transcriptomics.

https://github.com/deshpandelab/spacemarkers

Science Score: 49.0%

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 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    6 of 13 committers (46.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

An R/Bioconductor software tool to identify genes associated with latent space interactions in spatial transcriptomics.

Basic Info
  • Host: GitHub
  • Owner: DeshpandeLab
  • License: other
  • Language: R
  • Default Branch: main
  • Size: 24.7 MB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 5
  • Open Issues: 16
  • Releases: 2
Created about 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

SpaceMarkers

An R/Bioconductor software tool to identify genes associated with latent space interactions in spatial transcriptomics.

Citation

If you use the SpaceMarkers software please cite:

Atul Deshpande, Melanie Loth, et al., Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces. Cell Systems, April 2023. https://doi.org/10.1016/j.cels.2023.03.004

Installation

You can install the latest Bioconductor release from SpaceMarkers using the code below. ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("SpaceMarkers") You can install the development version of SpaceMarkers directly from the Github source. install.packages("remotes") remotes::installgithub("DeshpandeLab/SpaceMarkers", dependencies = TRUE, buildvignettes = TRUE) ```

Owner

  • Name: Deshpande Lab
  • Login: DeshpandeLab
  • Kind: organization

GitHub Events

Total
  • Create event: 12
  • Commit comment event: 1
  • Issues event: 15
  • Watch event: 1
  • Delete event: 13
  • Member event: 1
  • Issue comment event: 18
  • Push event: 80
  • Pull request event: 27
  • Pull request review event: 48
  • Pull request review comment event: 34
  • Fork event: 1
Last Year
  • Create event: 12
  • Commit comment event: 1
  • Issues event: 15
  • Watch event: 1
  • Delete event: 13
  • Member event: 1
  • Issue comment event: 18
  • Push event: 80
  • Pull request event: 27
  • Pull request review event: 48
  • Pull request review comment event: 34
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 270
  • Total Committers: 13
  • Avg Commits per committer: 20.769
  • Development Distribution Score (DDS): 0.685
Past Year
  • Commits: 57
  • Committers: 6
  • Avg Commits per committer: 9.5
  • Development Distribution Score (DDS): 0.561
Top Committers
Name Email Commits
atuldeshpande a****e@j****u 85
dimalvovs d****s@g****m 61
orian116 o****0@g****m 54
atuldeshpande a****e@g****m 29
dimalvovs d****1@j****u 15
Ludmila Danilova l****a@g****m 8
orian116 o****1@j****u 5
atuldeshpande a****4@w****u 4
orian116 5****6@u****m 3
J Wokaty j****y@s****u 2
J Wokaty j****y@u****m 2
ostaple1 o****n@E****l 1
ostaple1 o****n@e****u 1
Committer Domains (Top 20 + Academic)
jhu.edu: 2 eb-onc-1qywp45.acasmart.jh.edu: 1 sph.cuny.edu: 1 wisc.edu: 1 jh.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 23
  • Total pull requests: 53
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 26 days
  • Total issue authors: 4
  • Total pull request authors: 3
  • Average comments per issue: 0.78
  • Average comments per pull request: 0.3
  • Merged pull requests: 31
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 15
  • Pull requests: 38
  • Average time to close issues: 22 days
  • Average time to close pull requests: 10 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.93
  • Average comments per pull request: 0.42
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dimalvovs (14)
  • atuldeshpande (7)
  • orian116 (3)
  • mloberg16 (1)
Pull Request Authors
  • dimalvovs (30)
  • atuldeshpande (25)
  • orian116 (22)
Top Labels
Issue Labels
enhancement (1) good first issue (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 3,654 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: SpaceMarkers

Spatial Interaction Markers

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 3,654 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 31.3%
Average: 42.9%
Downloads: 97.4%
Maintainers (1)
adeshpande@jhu.edu
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • ape * depends
  • dplyr * depends
  • hdf5r * depends
  • jsonlite * depends
  • matrixStats * depends
  • matrixTests * depends
  • pracma * depends
  • rstatix * depends
  • spatstat * depends
  • Matrix * imports
  • qvalue * imports
  • spatstat.core * imports
  • spatstat.geom * imports
  • stats * imports
  • utils * imports
.github/workflows/main.yml actions
Dockerfile docker
  • rocker/tidyverse 4 build