EWCE

DOI: 10.18129/B9.bioc.EWCE    

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see EWCE.

Expression Weighted Celltype Enrichment

Bioconductor version: Development (3.14)

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

Author: Alan Murphy [cre] , Nathan Skene [aut]

Maintainer: Alan Murphy <alanmurph94 at hotmail.com>

Citation (from within R, enter citation("EWCE")):

Installation

To install this package, start R (version "4.1") and enter:

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

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

BiocManager::install("EWCE")

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("EWCE")

 

HTML R Script Expression Weighted Celltype Enrichment with EWCE
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray
Version 1.1.1
In Bioconductor since BioC 3.3 (R-3.3) (5.5 years)
License Artistic-2.0
Depends R (>= 4.1), RNOmni (>= 1.0)
Imports AnnotationHub, ewceData, ExperimentHub, ggplot2, grDevices, grid, reshape2, biomaRt, limma, stringr, cowplot, HGNChelper, ggdendro, gridExtra, Matrix, methods, parallel, future, scales, SummarizedExperiment, stats, utils
LinkingTo
Suggests devtools, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), data.table, sctransform, readxl, SingleCellExperiment, memoise, markdown
SystemRequirements
Enhances
URL https://github.com/NathanSkene/EWCE
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package EWCE_1.1.1.tar.gz
Windows Binary EWCE_1.1.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) EWCE_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/EWCE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EWCE
Package Short Url https://bioconductor.org/packages/EWCE/
Package Downloads Report Download Stats

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