EWCE

DOI: 10.18129/B9.bioc.EWCE  

This package is for version 3.17 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: 3.17

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] , Brian Schilder [aut] , Nathan Skene [aut]

Maintainer: Alan Murphy <alanmurph94 at hotmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

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	Extended examples
HTML	R Script	Getting started
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray
Version	1.8.2
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	GPL-3
Depends	R (>= 4.2), RNOmni (>= 1.0)
Imports	stats, utils, methods, ewceData(>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene(>= 0.99.8), data.table
LinkingTo
Suggests	rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork
SystemRequirements
Enhances
URL	https://github.com/NathanSkene/EWCE
BugReports	https://github.com/NathanSkene/EWCE/issues
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_1.8.2.tar.gz
Windows Binary	EWCE_1.8.2.zip (64-bit only)
macOS Binary (x86_64)	EWCE_1.8.2.tgz
macOS Binary (arm64)	EWCE_1.8.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EWCE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EWCE
Bioc Package Browser	https://code.bioconductor.org/browse/EWCE/
Package Short Url	https://bioconductor.org/packages/EWCE/
Package Downloads Report	Download Stats