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scDotPlot

Repository for the scDotPlot Bioconductor package

https://github.com/ben-laufer/scdotplot

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 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary

Keywords from Contributors

genomics bioconductor-package gene
Last synced: 10 months ago · JSON representation

Repository

Repository for the scDotPlot Bioconductor package

Basic Info
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created about 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

scDotPlot

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add multiple annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

Installation

scDotPlot can be installed from Bioconductor:

``` r if (!requireNamespace("BiocManager", quietly = TRUE)){ install.packages("BiocManager") }

BiocManager::install("scDotPlot") ```

To install the development version directly from GitHub:

```r if(!requireNamespace("remotes", quietly = TRUE)){ install.packages("remotes") }

remotes::install_github("ben-laufer/scDotPlot") ```

Examples

See the package vignette.

Owner

  • Name: Ben Laufer
  • Login: ben-laufer
  • Kind: user
  • Location: San Francisco, CA
  • Company: Genentech

Principal Scientist in the Department of OMNI Bioinformatics at Genentech.

GitHub Events

Total
  • Issues event: 2
  • Watch event: 7
  • Issue comment event: 2
  • Push event: 4
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 2
  • Watch event: 7
  • Issue comment event: 2
  • Push event: 4
  • Fork event: 1
  • Create event: 2

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 13
  • Total Committers: 3
  • Avg Commits per committer: 4.333
  • Development Distribution Score (DDS): 0.308
Past Year
  • Commits: 8
  • Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Ben Laufer l****n@g****m 9
A Wokaty a****y@s****u 2
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 gene.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 1 day
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 1 day
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • zhanzmr (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 2,938 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: scDotPlot

Cluster a Single-cell RNA-seq Dot Plot

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2,938 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 31.5%
Average: 42.2%
Downloads: 95.1%
Maintainers (1)
blaufer@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.4.0 depends
  • BiocGenerics * imports
  • Seurat * imports
  • SingleCellExperiment * imports
  • aplot * imports
  • cli * imports
  • dplyr * imports
  • ggplot2 * imports
  • ggsci * imports
  • ggtree * imports
  • grDevices * imports
  • magrittr * imports
  • purrr * imports
  • rlang * imports
  • scales * imports
  • scater * imports
  • stats * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • AnnotationDbi * suggests
  • SeuratObject * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • scRNAseq * suggests
  • scran * suggests
  • scuttle * suggests