ExpressionAtlas
This is the development version of ExpressionAtlas; for the stable release version, see ExpressionAtlas.
Search, download and visualise datasets from EMBL-EBI Expression Atlas and Single-Cell Expression Atlas
Bioconductor version: Development (3.21)
This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object. SingleCellExperiment object is used for Single-Cell Expression Atlas datasets.
Author: Pedro Madrigal [aut, cre]
, Anil Thanki [aut]
, Maria Keays [aut]
Maintainer: Pedro Madrigal <pmadrigal at ebi.ac.uk>
citation("ExpressionAtlas")):
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("ExpressionAtlas")
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("ExpressionAtlas")| Accessing data from Single-Cell Expression Atlas | HTML | R Script |
| Accessing GTEX RNA-seq data from Expression Atlas | HTML | R Script |
| ExpressionAtlas | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, SingleCellData, Software |
| Version | 1.99.4 |
| In Bioconductor since | BioC 3.3 (R-3.3) (9 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.4.0), methods, Biobase |
| Imports | utils, XML, httr, reshape2, tidyr, yaml, SummarizedExperiment, limma, SingleCellExperiment, viridis, HDF5Array, S4Vectors, xml2, jsonlite, BiocStyle, zellkonverter, gplots, genefilter, edgeR, ggplot2, dplyr, ComplexHeatmap, circlize |
| System Requirements | |
| URL | https://github.com/ebi-gene-expression-group/bioconductor-ExpressionAtlas |
| Bug Reports | https://github.com/ebi-gene-expression-group/bioconductor-ExpressionAtlas/issues |
See More
| Suggests | knitr, testthat, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | spatialHeatmap |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ExpressionAtlas_1.99.4.tar.gz |
| Windows Binary (x86_64) | ExpressionAtlas_1.99.4.zip |
| macOS Binary (x86_64) | ExpressionAtlas_1.99.4.tgz |
| macOS Binary (arm64) | ExpressionAtlas_1.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ExpressionAtlas |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ExpressionAtlas |
| Bioc Package Browser | https://code.bioconductor.org/browse/ExpressionAtlas/ |
| Package Short Url | https://bioconductor.org/packages/ExpressionAtlas/ |
| Package Downloads Report | Download Stats |