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scpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.

https://github.com/enblacar/scpubr

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 1 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 (18.8%) to scientific vocabulary

Keywords

data-visualization ggplot2 publication-quality-plots r rstats seurat single-cell single-cell-genomics single-cell-rna-seq visualization
Last synced: 6 months ago · JSON representation

Repository

Generate high quality, publication ready visualizations for single cell transcriptomics data.

Basic Info
Statistics
  • Stars: 204
  • Watchers: 4
  • Forks: 13
  • Open Issues: 1
  • Releases: 24
Topics
data-visualization ggplot2 publication-quality-plots r rstats seurat single-cell single-cell-genomics single-cell-rna-seq visualization
Created about 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

SCpubr

CRAN status R-CMD-check Code Coverage CodeFactor metacran downloads <!-- badges: end -->

SCpubr provides a streamlined way of generating publication ready plots for known Single-Cell visualizations in a "publication ready" format (SCpubr). This is, the aim is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.

Installation

SCpubr can be installed via:

```r

From CRAN - Official release:

install.packages("SCpubr")

From GitHub - Latest stable development version:

if(!requireNamespace("devtools", quietly = TRUE)){ install.packages("devtools") # If not installed. }

devtools::install_github("enblacar/SCpubr", ref = "v2.0.0-dev-stable") ```

By default, SCpubr downloads without installing any of the required dependencies. A comprehensive report of which dependencies are still missing and which functions can be run is available through:

r SCpubr::package_report(extended = TRUE)

For tutorials, check SCpubr's reference manual.

Updates

SCpubr is an active package currently aiming to improve and add new functionalities.

Keep track of our new updates in the NEWS page!

Citation

To cite SCpubr in your publications, please use:

Blanco-Carmona, E. Generating publication ready visualizations for Single Cell transcriptomics using SCpubr. bioRxiv (2022) doi:10.1101/2022.02.28.482303.

Contact

scpubr@gmail.com

Owner

  • Name: Enrique Blanco Carmona
  • Login: enblacar
  • Kind: user
  • Location: Heidelberg, Germany
  • Company: DKFZ

PhD Student in Bioinformatics.

GitHub Events

Total
  • Issues event: 22
  • Watch event: 42
  • Issue comment event: 45
  • Push event: 19
  • Fork event: 3
Last Year
  • Issues event: 22
  • Watch event: 42
  • Issue comment event: 45
  • Push event: 19
  • Fork event: 3

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 741
  • Total Committers: 4
  • Avg Commits per committer: 185.25
  • Development Distribution Score (DDS): 0.012
Past Year
  • Commits: 42
  • Committers: 2
  • Avg Commits per committer: 21.0
  • Development Distribution Score (DDS): 0.167
Top Committers
Name Email Commits
enblacar e****a@d****e 732
nbpeterson3 6****3 7
Paul Hoffman p****n@t****m 1
Safwat Khan s****n@m****a 1
Committer Domains (Top 20 + Academic)
mail.utoronto.ca: 1 tiledb.com: 1 dkfz-heidelberg.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 82
  • Total pull requests: 4
  • Average time to close issues: 13 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 60
  • Total pull request authors: 4
  • Average comments per issue: 2.5
  • Average comments per pull request: 1.5
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 12
  • Pull requests: 0
  • Average time to close issues: 13 days
  • Average time to close pull requests: N/A
  • Issue authors: 12
  • Pull request authors: 0
  • Average comments per issue: 1.17
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • TdzBAS (6)
  • ccruizm (6)
  • aditisk (4)
  • frac2738 (3)
  • dfernandezperez (2)
  • shahrozeabbas (2)
  • athulmenon (2)
  • hmlopezbertoni (2)
  • kaizen89 (2)
  • npotemkin (2)
  • mojaveazure (1)
  • jcshuy (1)
  • isaiao01 (1)
  • dbdimitrov (1)
  • KalinNonchev (1)
Pull Request Authors
  • nbpeterson3 (3)
  • Safwat08 (2)
  • Christian-Heyer (1)
  • mojaveazure (1)
Top Labels
Issue Labels
enhancement (8) bug (4) question (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • cran 867 last-month
  • Total docker downloads: 130
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 52
  • Total maintainers: 1
proxy.golang.org: github.com/enblacar/scpubr
  • Versions: 20
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.3%
Average: 5.4%
Dependent repos count: 5.6%
Last synced: 6 months ago
proxy.golang.org: github.com/enblacar/SCpubr
  • Versions: 20
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
cran.r-project.org: SCpubr

Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 867 Last month
  • Docker Downloads: 130
Rankings
Stargazers count: 3.8%
Forks count: 9.6%
Downloads: 16.2%
Average: 16.6%
Docker downloads count: 17.3%
Dependent repos count: 24.0%
Dependent packages count: 28.8%
Maintainers (1)
scpubr@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • ComplexHeatmap * suggests
  • Matrix * suggests
  • Nebulosa * suggests
  • Seurat * suggests
  • SeuratObject * suggests
  • circlize * suggests
  • colorspace * suggests
  • covr * suggests
  • dplyr * suggests
  • enrichR * suggests
  • forcats * suggests
  • ggExtra * suggests
  • ggbeeswarm * suggests
  • ggplot2 * suggests
  • ggpubr * suggests
  • ggrastr * suggests
  • ggrepel * suggests
  • ggtext * suggests
  • knitr * suggests
  • patchwork * suggests
  • pbapply * suggests
  • pheatmap * suggests
  • purrr * suggests
  • qpdf * suggests
  • rlang * suggests
  • rmarkdown * suggests
  • scales * suggests
  • stringr * suggests
  • svglite * suggests
  • testthat >= 3.0.0 suggests
  • tidyr * suggests
  • viridis * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 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
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite