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: Development (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:
Maintainer: Alan Murphy <alanmurph94 at hotmail.com>
citation("EWCE")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 |
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.
| Source Package | EWCE_1.15.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |