DOI: 10.18129/B9.bioc.EWCE  

This package is for version 3.16 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: 3.16

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")):


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biocViews BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray
Version 1.6.0
In Bioconductor since BioC 3.3 (R-3.3) (7 years)
License GPL-3
Depends R (>= 4.2), RNOmni (>= 1.0)
Imports stats, utils, methods, ewceData, dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene(>= 0.99.8), data.table
Suggests remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, cowplot, ggdendro, grDevices, grid, gridExtra, scales, magick, badger
URL https://github.com/NathanSkene/EWCE
BugReports https://github.com/NathanSkene/EWCE/issues
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Source Package EWCE_1.6.0.tar.gz
Windows Binary EWCE_1.6.0.zip (64-bit only)
macOS Binary (x86_64) EWCE_1.6.0.tgz
macOS Binary (arm64) EWCE_1.6.0.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/
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