EWCE

This is the development version of EWCE; for the stable release version, see EWCE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.5, 3.4, 3.3

Expression Weighted Celltype Enrichment

Bioconductor version: Development (3.24)

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 [aut] ORCID: 0000-0002-2487-8753 , Brian Schilder [aut] ORCID: 0000-0001-5949-2191 , Hiranyamaya Dash [cre] ORCID: 0009-0005-5514-505X , Nathan Skene [aut] ORCID: 0000-0002-6807-3180

Maintainer: Hiranyamaya Dash <hdash.work at gmail.com>

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

Alan Murphy, Brian Schilder, Nathan Skene. EWCE: Expression Weighted Celltype Enrichment. doi:10.18129/B9.bioc.EWCE, R package version 1.21.0, https://bioconductor.org/packages/EWCE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray
Version	1.21.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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
System Requirements
URL	https://github.com/NathanSkene/EWCE
Bug Reports	https://github.com/NathanSkene/EWCE/issues

Suggests	rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	EWCE_1.21.0.tar.gz
Windows Binary (x86_64)	EWCE_1.21.0.zip
macOS Binary (big-sur-x86_64)	EWCE_1.21.0.tgz
macOS Binary (sonoma-arm64)	EWCE_1.21.0.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