cellNexus
This is the development version of cellNexus; to use it, please install the devel version of Bioconductor.
Queries the Human Cell Atlas
Bioconductor version: Development (3.24)
Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into one of several supported formats, including SingleCellExperiment, Seurat, or pseudobulk SummarizedExperiment objects. Note: The Human Cell Atlas data accessed through this package is subject to its own licensing terms (typically Creative Commons Attribution or similar open data licenses as specified by the Human Cell Atlas Data Use Agreement), which differ from the package license (GPL-3). See the package documentation for details.
Author: Stefano Mangiola [aut, rev, ctb]
, Mengyuan Shen [aut, cre, rev]
, Michael Milton [aut, rev, ctb]
, Jared Andrews [aut, rev, ctb], Juan Henao [aut, ctb], Edward Yang [aut, ctb], Julie Iskander [rev], Silicon Valley Foundation CZF2019-002443 [fnd], NIH NHGRI 5U24HG004059-18 [fnd], Victoria Cancer Agency ECRF21036 [fnd], NHMRC 1116955 [fnd]
Maintainer: Mengyuan Shen <shen.m at wehi.edu.au>
citation("cellNexus")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("cellNexus")
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("cellNexus")| cellNexus | HTML |
| Gene Expression Explore | HTML |
| Metadata Explore | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, ShinyApps, SingleCell, Software, Transcription, Transcriptomics |
| Version | 0.99.23 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, curl, cli, SeuratObject, Seurat, methods, rlang, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, checkmate, shiny, shinyWidgets, zellkonverter, anndataR, stringr, Matrix, rclipboard |
| System Requirements | Python |
| URL | https://github.com/MangiolaLaboratory/cellNexus https://mangiolalaboratory.github.io/cellNexus/ |
| Bug Reports | https://github.com/MangiolaLaboratory/cellNexus/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, rprojroot, openssl, DelayedArray, tidybulk, BiocParallel, preprocessCore |
| 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 | cellNexus_0.99.23.tar.gz |
| Windows Binary (x86_64) | cellNexus_0.99.23.zip |
| macOS Binary (big-sur-x86_64) | cellNexus_0.99.23.tgz |
| macOS Binary (sonoma-arm64) | cellNexus_0.99.23.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cellNexus |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cellNexus |
| Bioc Package Browser | https://code.bioconductor.org/browse/cellNexus/ |
| Package Short Url | https://bioconductor.org/packages/cellNexus/ |
| Package Downloads Report | Download Stats |