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EWCE

This package is for version 3.19 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 (3.19)

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>

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

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

Details

biocViews BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray
Version 1.11.5
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL https://github.com/NathanSkene/EWCE
Bug Reports https://github.com/NathanSkene/EWCE/issues
See More
Suggests rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork
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Package Archives

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

Source Package EWCE_1.11.5.tar.gz
Windows Binary EWCE_1.11.5.zip
macOS Binary (x86_64) EWCE_1.11.5.tgz
macOS Binary (arm64) EWCE_1.11.5.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