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Bioconductor - EWCE

EWCE

This package is for version 3.21 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: Release (3.21)

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] ORCID: 0000-0002-2487-8753 , Brian Schilder [aut] ORCID: 0000-0001-5949-2191 , Nathan Skene [aut] ORCID: 0000-0002-6807-3180

Maintainer: Alan Murphy <alanmurph94 at hotmail.com>

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

To install this package, start R (version "4.5") 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")

Details biocViews BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray Version 1.16.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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