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CuratedAtlasQueryR

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

Queries the Human Cell Atlas


Bioconductor version: Development (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 (from within R, enter citation("CuratedAtlasQueryR")):

Installation

To install this package, start R (version "4.4") 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

Details

biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.1.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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
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Depends On Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CuratedAtlasQueryR_1.1.1.tar.gz
Windows Binary CuratedAtlasQueryR_1.1.1.zip
macOS Binary (x86_64) CuratedAtlasQueryR_1.1.1.tgz
macOS Binary (arm64) CuratedAtlasQueryR_1.1.1.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