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EWCE

Expression Weighted Celltype Enrichment

Bioconductor version: 3.23 · Package version: 1.20.0

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.

Installation

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

BiocManager::install("EWCE")

Details

MaintainerHiranyamaya Dash <hdash.work@gmail.com>
AuthorAlan Murphy [aut] (ORCID: <https://orcid.org/0000-0002-2487-8753>), Brian Schilder [aut] (ORCID: <https://orcid.org/0000-0001-5949-2191>), Hiranyamaya Dash [cre] (ORCID: <https://orcid.org/0009-0005-5514-505X>), Nathan Skene [aut] (ORCID: <https://orcid.org/0000-0002-6807-3180>)
LicenseGPL-3
URLhttps://github.com/NathanSkene/EWCE
Bug Reportshttps://github.com/NathanSkene/EWCE/issues
Downloads rank628
Source branchRELEASE_3_23
biocViewsBiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageEWCE_1.20.0.tar.gz
Windows binary (x86_64)EWCE_1.20.0.zip
macOS binary (arm64)EWCE_1.20.0.tgz
macOS binary (x86_64)EWCE_1.20.0.tgz
Dependencies

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

Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork