EWCE: Expression Weighted Celltype Enrichment

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
Dr Nathan Skene
Date of publication
None
Maintainer
Nathan Skene <nathan.skene@gmail.com>
License
Artistic-2.0
Version
1.2.0

View on Bioconductor

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)

Files in this package

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