Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Keywords from Contributors
Repository
R interface to the cellxgene data portal
Basic Info
- Host: GitHub
- Owner: mtmorgan
- Language: R
- Default Branch: devel
- Homepage: https://mtmorgan.github.io/cellxgenedp/
- Size: 8.3 MB
Statistics
- Stars: 8
- Watchers: 5
- Forks: 5
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
Introduction to cellxgenedp
The cellxgene data portal https://cellxgene.cziscience.com/ provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.
Installation
This package is available in Bioconductor version 3.15 and later. The following code installs cellxgenedp
r
if (!"BiocManager" %in% rownames(installed.packages()))
install.packages("BiocManager", repos = "https://CRAN.R-project.org")
BiocManager::install("cellxgenedp")
Alternatively, install the 'development' version from GitHub
r
if (!"remotes" %in% rownames(installed.packages()))
install.packages("remotes", repos = "https://CRAN.R-project.org")
remotes::install_github("mtmorgan/cellxgenedp")
To also install additional packages required for this vignette, use
r
pkgs <- c("tidyr", "zellkonverter", "SingleCellExperiment", "HDF5Array")
required_pkgs <- pkgs[!pkgs %in% rownames(installed.packages())]
BiocManager::install(required_pkgs)
Use
Load the package into your current R session. We make extensive use of the dplyr packages, and at the end of the vignette use SingleCellExperiment and zellkonverter, so load those as well.
r
suppressPackageStartupMessages({
library(dplyr)
library(cellxgenedp)
})
Shiny
cxg() provides a ‘shiny’ interface allowing discovery of collections
and datasets, visualization of selected datasets in the cellxgene data
portal, and download of datasets for use in R.
Next steps
View the artcle Discover and download datasets and files from the cellxgene data portal.
Owner
- Name: Martin Morgan
- Login: mtmorgan
- Kind: user
- Location: Buffalo, NY
- Website: https://bioconductor.org
- Repositories: 33
- Profile: https://github.com/mtmorgan
GitHub Events
Total
- Push event: 1
- Create event: 1
Last Year
- Push event: 1
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 9
- Total pull requests: 8
- Average time to close issues: 5 days
- Average time to close pull requests: 13 days
- Total issue authors: 6
- Total pull request authors: 5
- Average comments per issue: 1.67
- Average comments per pull request: 0.38
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: 3 days
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- stemangiola (3)
- vjcitn (2)
- LiNk-NY (1)
- YXC33 (1)
- suresh-advaitabio (1)
- lgatto (1)
Pull Request Authors
- Kayla-Morrell (4)
- vjcitn (1)
- mtmorgan (1)
- LiNk-NY (1)
- stemangiola (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 9,315 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: cellxgenedp
Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
- Homepage: https://mtmorgan.github.io/cellxgenedp/ https://github.com/mtmorgan/cellxgenedp
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/cellxgenedp/inst/doc/cellxgenedp.pdf
- License: Artistic-2.0
-
Latest release: 1.12.1
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- DT * imports
- curl * imports
- dplyr * imports
- httr * imports
- jsonlite * imports
- shiny * imports
- tools * imports
- utils * imports
- BiocStyle * suggests
- HDF5Array * suggests
- SingleCellExperiment * suggests
- knitr * suggests
- mockery * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- zellkonverter * suggests
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-renv v1 composite