README.md

In robertamezquita/Inkwell: Containers for Curated Cell Type Signatures

output: github_document

Inkwell

The goal of Inkwell is to provide a collection of curated cell-type specific genesets for use in (manual) classification of single-cell RNA-seq data. For methods on assigning these signatures to cells, see Hancock.

Installation

You can install Inkwell from Github with:

devtools::install_github("robertamezquita/Inkwell")

Usage

Inkwell stores curated genesets derived from online resources and publications for use with outside methods of annotation. This package makes use of the Bioconductor GSEABase to store signatures as GeneSetCollection and GeneSet class objects. For more details, check out the associated vignette and reference manual.

Briefly, stored genesets are provided as data provided upon loading Inkwell.

library(Inkwell)
MCPcounter_markers
#> GeneSetCollection
#>   names: T cells, CD8 T cells, ..., Fibroblasts (10 total)
#>   unique identifiers: CD28, CD3D, ..., TAGLN (111 total)
#>   types in collection:
#>     geneIdType: SymbolIdentifier (1 total)
#>     collectionType: NullCollection (1 total)

Creating Your Own Genesets

To create your own genesets, see data-raw/template.R for a quick template on essential fields and descriptions for creating a manually curated GeneSetCollection, and the data-raw/pbmc3k_markers.R script for how the example pbmc3k_markers data object was created.

Looking Forward

Future iterations will utilize additional capabilities of the GSEABase package provided classes, such as GeneColorSet to provide additional annotation of genes such as expression status or confidence estimates. Furthermore, in addition to manually curated sets, select calculated sets may be included in future iterations, which could include such additional rich information about (differential) expression status.

Methods to create and cache genesets may also be implemented in future iterations to expand the scope of the package beyond manually curated genesets.

Available Genesets

Below are the data available in the package, where the data column refers to the object that is accessible upon loading Inkwell.

| data | description | source | |------------------|------------------------------------------------------------------------|---------------------------------------------------| | pbmc3k_markers | Markers from Satija lab tutorial for Seurat using PBMC 3k 10X dataset. | https://satijalab.org/seurat/pbmc3k_tutorial.html | | MCPcounter_markers | Markers from Becht et al. 2016 defining major canonical cell-types | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1070-5 |

robertamezquita/Inkwell documentation built on May 17, 2019, 10:13 a.m.