cellxgenedp
This is the development version of cellxgenedp; for the stable release version, see cellxgenedp.
Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
Bioconductor version: Development (3.24)
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 interface, allowing data discovery, viewing, and downloading.
Author: Martin Morgan [aut, cre]
, Kayla Interdonato [aut]
Maintainer: Martin Morgan <mtmorgan.bioc at gmail.com>
citation("cellxgenedp")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("cellxgenedp")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cellxgenedp")| Case studies | HTML | R Script |
| Discovery and retrieval | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, SingleCell, Software, ThirdPartyClient |
| Version | 1.17.1 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), dplyr |
| Imports | httr, curl, utils, tools, cli, shiny, DT, rjsoncons |
| System Requirements | |
| URL | https://mtmorgan.github.io/cellxgenedp/ https://github.com/mtmorgan/cellxgenedp |
| Bug Reports | https://github.com/mtmorgan/cellxgenedp/issues |
See More
| Suggests | zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cellxgenedp_1.17.1.tar.gz |
| Windows Binary (x86_64) | cellxgenedp_1.17.1.zip |
| macOS Binary (big-sur-x86_64) | cellxgenedp_1.17.1.tgz |
| macOS Binary (sonoma-arm64) | cellxgenedp_1.17.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cellxgenedp |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cellxgenedp |
| Bioc Package Browser | https://code.bioconductor.org/browse/cellxgenedp/ |
| Package Short Url | https://bioconductor.org/packages/cellxgenedp/ |
| Package Downloads Report | Download Stats |