xCellData

The goal of xCellData is to provide a R / Bioconductor resource for obtaining and representing 489 cell type gene signatures from Aran et al., 2017.

Prerequisites

The xCellData package uses the BaseSets class defined in the unisets package. This dependency may be installed as follows:

install.packages("devtools")
devtools::install_github("kevinrue/unisets", build_opts = c("--no-resave-data", "--no-manual"))

Installation

You can install the released version of xCellData from GitHub with:

install.packages("devtools")
devtools::install_github("kevinrue/xCellData")

Example

This is a basic example which shows you how to load the signatures into your R session.

library(xCellData)
object <- xCellData()
object

BaseSets with 20803 relations between 5079 elements and 489 sets
     element          set relationData elementData                                   setData
  <IdVector>   <IdVector>  <DataFrame> <DataFrame>                               <DataFrame>
1       C1QA   aDC_HPCA_1                          https://doi.org/10.1186/s13059-017-1349-1
2       C1QB   aDC_HPCA_1                          https://doi.org/10.1186/s13059-017-1349-1
3      CCL13   aDC_HPCA_1                          https://doi.org/10.1186/s13059-017-1349-1
4      CCL17   aDC_HPCA_1                          https://doi.org/10.1186/s13059-017-1349-1
5      CCL19   aDC_HPCA_1                          https://doi.org/10.1186/s13059-017-1349-1
         ...          ...          ...         ...                                       ...
1      IL2RA Tregs_HPCA_3                          https://doi.org/10.1186/s13059-017-1349-1
2      KCNA2 Tregs_HPCA_3                          https://doi.org/10.1186/s13059-017-1349-1
3      LAIR2 Tregs_HPCA_3                          https://doi.org/10.1186/s13059-017-1349-1
4     MCF2L2 Tregs_HPCA_3                          https://doi.org/10.1186/s13059-017-1349-1
5       RGS1 Tregs_HPCA_3                          https://doi.org/10.1186/s13059-017-1349-1