CuratedAtlasQueryR

This is the development version of CuratedAtlasQueryR; for the stable release version, see CuratedAtlasQueryR.

Queries the Human Cell Atlas

Bioconductor version: Development (3.21)

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] (ORCID: ), Michael Milton [aut, rev] (ORCID: ), 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 (from within R, enter citation("CuratedAtlasQueryR")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.3.0
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

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_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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