CuratedAtlasQueryR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CuratedAtlasQueryR.
Queries the Human Cell Atlas
Bioconductor version: 3.19
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 a SingleCellExperiment object.
Author: Stefano Mangiola [aut, cre, rev] 
, Michael Milton [aut, rev] , Martin Morgan [ctb, rev], Vincent Carey [ctb, rev], Julie Iskander [rev], Tony Papenfuss [rev], Silicon Valley Foundation CZF2019-002443 [fnd], NIH NHGRI 5U24HG004059-18 [fnd], Victoria Cancer Agency ECRF21036 [fnd], NHMRC 1116955 [fnd]
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
citation("CuratedAtlasQueryR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CuratedAtlasQueryR")
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("CuratedAtlasQueryR")| CuratedAtlasQueryR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr |
| System Requirements | |
| URL | https://github.com/stemangiola/CuratedAtlasQueryR |
| Bug Reports | https://github.com/stemangiola/CuratedAtlasQueryR/issues |
See More
| Suggests | zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot |
| 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 | CuratedAtlasQueryR_1.2.0.tar.gz |
| Windows Binary (x86_64) | CuratedAtlasQueryR_1.2.0.zip |
| macOS Binary (x86_64) | CuratedAtlasQueryR_1.2.0.tgz |
| macOS Binary (arm64) | CuratedAtlasQueryR_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CuratedAtlasQueryR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CuratedAtlasQueryR |
| Bioc Package Browser | https://code.bioconductor.org/browse/CuratedAtlasQueryR/ |
| Package Short Url | https://bioconductor.org/packages/CuratedAtlasQueryR/ |
| Package Downloads Report | Download Stats |