EWCE: Expression Weighted Celltype Enrichment
Version 1.3.0

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.

AuthorDr Nathan Skene
Bioconductor views BiomedicalInformatics DifferentialExpression FunctionalGenomics GeneExpression GeneSetEnrichment Genetics Microarray OneChannel Proteomics RNASeq Transcription Visualization mRNAMicroarray
Date of publicationNone
MaintainerNathan Skene <nathan.skene@gmail.com>
LicenseArtistic-2.0
Version1.3.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EWCE")

Getting started

Expression Weighted Celltype Enrichment with *EWCE*

Popular man pages

bootstrap.enrichment.test: Bootstrap celltype enrichment test
celltype_data: Subset of genes from Linnarsson lab's cortex single cell...
example_genelist: Example Gene list
mouse_to_human_homologs: Table of Human->Mouse orthologs for all human genes
read_celltype_data: Read single cell transcriptome data
tt_alzh: Example table of differential expression (Alzheimer's BA46)
tt_alzh_BA44: Example table of differential expression (Alzheimer's BA44)
See all...

All man pages Function index File listing

Man pages

add.res.to.merging.list: Add to results to merging list
bootstrap.enrichment.test: Bootstrap celltype enrichment test
celltype_data: Subset of genes from Linnarsson lab's cortex single cell...
ewce_expression_data: Bootstrap celltype enrichment test for transcriptome data
ewce.plot: Plot EWCE results
example_genelist: Example Gene list
generate.bootstrap.plots: Generate bootstrap plots
merged_ewce: Multiple EWCE results from multiple studies
mouse_to_human_homologs: Table of Human->Mouse orthologs for all human genes
read_celltype_data: Read single cell transcriptome data
tt_alzh: Example table of differential expression (Alzheimer's BA46)
tt_alzh_BA36: Example table of differential expression (Alzheimer's BA36)
tt_alzh_BA44: Example table of differential expression (Alzheimer's BA44)

Functions

Files

DESCRIPTION
NAMESPACE
R
R/add.res.to.merging.list.R
R/bootstrap.enrichment.test.R
R/cell.list.dist.R
R/data.R
R/ewce.plot.R
R/ewce_expression_data.R
R/generate.bootstrap.plots.R
R/merged_ewce.R
R/prepare.genesize.control.network.R
R/read_celltype_data.R
R/subcell.list.dist.R
build
build/vignette.rds
data
data/celltype_data.rda
data/datalist
data/example_genelist.rda
data/mouse_to_human_homologs.rda
data/tt_alzh.rda
data/tt_alzh_BA36.rda
data/tt_alzh_BA44.rda
inst
inst/doc
inst/doc/EWCE.R
inst/doc/EWCE.Rmd
inst/doc/EWCE.html
man
man/add.res.to.merging.list.Rd
man/bootstrap.enrichment.test.Rd
man/celltype_data.Rd
man/ewce.plot.Rd
man/ewce_expression_data.Rd
man/example_genelist.Rd
man/generate.bootstrap.plots.Rd
man/merged_ewce.Rd
man/mouse_to_human_homologs.Rd
man/read_celltype_data.Rd
man/tt_alzh.Rd
man/tt_alzh_BA36.Rd
man/tt_alzh_BA44.Rd
vignettes
vignettes/BootstrapPlots
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_.none..pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Epend.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____endothelial.mural_Vsmc.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Mgl1.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Mgl2.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Pvm1.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Pvm2.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____oligodendrocytes_Oligo2.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____oligodendrocytes_Oligo3.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____oligodendrocytes_Oligo6.pdf
vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_.none..pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Epend.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____endothelial.mural_Vsmc.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Mgl1.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Mgl2.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Pvm1.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Pvm2.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____oligodendrocytes_Oligo2.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____oligodendrocytes_Oligo3.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____oligodendrocytes_Oligo6.pdf
vignettes/BootstrapPlots/bootDists____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_.none..pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Epend.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____endothelial.mural_Vsmc.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Mgl1.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Mgl2.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Pvm1.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Pvm2.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____oligodendrocytes_Oligo2.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____oligodendrocytes_Oligo3.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____oligodendrocytes_Oligo6.pdf
vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_.none..pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Epend.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____endothelial.mural_Vsmc.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Mgl1.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Mgl2.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Pvm1.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Pvm2.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____oligodendrocytes_Oligo2.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____oligodendrocytes_Oligo3.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____oligodendrocytes_Oligo6.pdf
vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
vignettes/EWCE.Rmd
vignettes/EWCE.bib
vignettes/EWCE_cache
vignettes/EWCE_cache/html
vignettes/EWCE_cache/html/__packages
vignettes/EWCE_cache/html/unnamed-chunk-14_4411e5f4113b952f3920425bdf252363.RData
vignettes/EWCE_cache/html/unnamed-chunk-14_4411e5f4113b952f3920425bdf252363.rdb
vignettes/EWCE_cache/html/unnamed-chunk-14_4411e5f4113b952f3920425bdf252363.rdx
vignettes/nature.csl
EWCE documentation built on May 20, 2017, 10:44 p.m.

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