CuratedAtlasQueryR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see CuratedAtlasQueryR.

Queries the Human Cell Atlas

DOI: 10.18129/B9.bioc.CuratedAtlasQueryR

Bioconductor version: 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 iD ORCID: 0000-0001-7474-836X , Michael Milton [aut, rev] ORCID iD ORCID: 0000-0002-8965-2595 , 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")
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 1.6.0

In Bioconductor since BioC 3.18 (R-4.3) (2 years)

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_1.6.0.tar.gz

Windows Binary (x86_64) CuratedAtlasQueryR_1.6.0.zip

macOS Binary (x86_64) CuratedAtlasQueryR_1.6.0.tgz

macOS Binary (arm64) CuratedAtlasQueryR_1.6.0.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