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sccustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

https://github.com/samuel-marsh/sccustomize

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 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.0%) to scientific vocabulary

Keywords

customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization
Last synced: 6 months ago · JSON representation

Repository

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Basic Info
Statistics
  • Stars: 271
  • Watchers: 2
  • Forks: 28
  • Open Issues: 7
  • Releases: 18
Topics
customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.md

scCustomize

CRAN Version CRAN Downloads R-CMD-check license issues DOI

scCustomize is a collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Vignettes/Tutorials

See accompanying scCustomize website for detailed tutorials of all aspects of scCustomize functionality.

Installing scCustomize

scCustomize can be installed from CRAN on all platforms. For more detailed instructions see Installation.

# Base R
install.packages("scCustomize")

# Using pak
pak::pkg_install("scCustomize")

Release Notes

A full copy of the changes in each version can be found in the NEWS/ChangeLog.

Develop branch
I also maintain a separate development branch* that can be installed by supplying ref = "develop" in the devtools or remotes installation command. Version scheme vX.X.X.9yyy.
*Note: While this branch is typically mostly stable it may contain breaking issues/bugs.
I do try and keep development ChangeLog up to date so it’s easier to follow changes than reading commit history.

Bug Reports/New Features

If you run into any issues or bugs please submit a GitHub issue with details of the issue.

  • If possible please include a reproducible example (suggest using SeuratData package pbmc dataset for lightweight examples.)

Any requests for new features or enhancements can also be submitted as GitHub issues.

  • Even if you don’t know how to implement/incorporate with current package go ahead a submit!

Pull Requests are welcome for bug fixes, new features, or enhancements.

  • Please set PR to merge with “develop” branch and provide description of what the PR contains (referencing existing issue(s) if appropriate).

Owner

  • Name: Samuel Marsh
  • Login: samuel-marsh
  • Kind: user
  • Location: Boston, MA
  • Company: Boston Childrens Hospital/HMS/Broad Institute

Postdoctoral Fellow. Interested in Neuroimmunology, Single Cell, and Neurodegenerative Disease

GitHub Events

Total
  • Create event: 6
  • Release event: 2
  • Issues event: 51
  • Watch event: 59
  • Delete event: 2
  • Issue comment event: 81
  • Push event: 225
  • Pull request event: 5
  • Fork event: 7
Last Year
  • Create event: 6
  • Release event: 2
  • Issues event: 51
  • Watch event: 59
  • Delete event: 2
  • Issue comment event: 81
  • Push event: 225
  • Pull request event: 5
  • Fork event: 7

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 3,075
  • Total Committers: 4
  • Avg Commits per committer: 768.75
  • Development Distribution Score (DDS): 0.001
Past Year
  • Commits: 343
  • Committers: 1
  • Avg Commits per committer: 343.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
samuel-marsh s****h@c****u 3,072
kew24 k****a@v****g 1
Paul Hoffman m****e 1
Maëlle Salmon m****n@y****e 1
Committer Domains (Top 20 + Academic)
vai.org: 1 childrens.harvard.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 196
  • Total pull requests: 30
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 19 days
  • Total issue authors: 117
  • Total pull request authors: 7
  • Average comments per issue: 3.31
  • Average comments per pull request: 0.47
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 30
  • Pull requests: 6
  • Average time to close issues: 8 days
  • Average time to close pull requests: about 1 month
  • Issue authors: 26
  • Pull request authors: 2
  • Average comments per issue: 1.7
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • samuel-marsh (53)
  • nikofleischer (5)
  • jasonleongbio (4)
  • giorgiatosoni (4)
  • ishwarvh (3)
  • mph270 (3)
  • CroixJeremy2 (3)
  • denvercal1234GitHub (3)
  • SimoniMD (2)
  • rhart604 (2)
  • eadaui (2)
  • williamsdrake (2)
  • BaptLabRight (2)
  • Flu09 (2)
  • levinhein (2)
Pull Request Authors
  • samuel-marsh (23)
  • fbearoff (2)
  • maelle (1)
  • mustafapir (1)
  • crazyhottommy (1)
  • mojaveazure (1)
  • kew24 (1)
Top Labels
Issue Labels
enhancement (48) bug (32) New Feature (21) Not Working As Intended (19) Vignette Related (16) Release Prep (15) more-info-needed (11) documentation (11) Help Wanted (1) Return Later New/Updated Feature? (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • cran 2,534 last-month
  • Total docker downloads: 935
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 48
  • Total maintainers: 1
proxy.golang.org: github.com/samuel-marsh/scCustomize
  • Versions: 18
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/samuel-marsh/sccustomize
  • Versions: 18
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
cran.r-project.org: scCustomize

Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2,534 Last month
  • Docker Downloads: 935
Rankings
Stargazers count: 3.9%
Forks count: 5.3%
Downloads: 13.9%
Average: 17.7%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
sccustomize@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Seurat >= 4.0.6 depends
  • Matrix * imports
  • Seurat >= 4.0.5 imports
  • SeuratObject >= 4.0.3 imports
  • circlize * imports
  • colorway * imports
  • cowplot * imports
  • data.table * imports
  • dittoSeq * imports
  • dplyr * imports
  • forcats * imports
  • ggbeeswarm * imports
  • ggplot2 * imports
  • ggprism * imports
  • ggpubr * imports
  • ggrastr * imports
  • ggrepel * imports
  • glue * imports
  • grid * imports
  • janitor * imports
  • magrittr * imports
  • paletteer * imports
  • patchwork * imports
  • pbapply * imports
  • purrr * imports
  • remotes >= 2.4.0 imports
  • scales * imports
  • scattermore >= 0.7 imports
  • stringi * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • tidyselect * imports
  • viridis * imports
  • ComplexHeatmap * suggests
  • DropletUtils * suggests
  • Nebulosa * suggests
  • knitr * suggests
  • qs * suggests
  • rliger * suggests
  • rmarkdown * suggests
  • tidyverse * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite