README.md

In flaviusb/homosapienDEE2CellScore: Example Data Package for CellScore

homosapienDEE2CellScore

Example packaged cell data

Requirements

This package requires Bioconductor version 3.17 or later, as that version is when the data of this data package was added to ExperimentHub. That in turn requires R version 4.3.0.

Installation

This package is not yet uploaded to Bioconductor; in order to install it from this git repo, first clone the repo:

git clone https://github.com/flaviusb/homosapienDEE2CellScore.git

Then, run R inside the cloned directory. In order to load the package locally, you need to set things up like so:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
install.packages("devtools")
BiocManager::install()
BiocManager::install("getDEE2")
BiocManager::install("DESeq2")
library(DESeq2)
library(Biobase)
library(SummarizedExperiment)
library(getDEE2)
library(devtools)
devtools::install_github(repo="flaviusb/CellScore")
library(CellScore)

And then you can run the following to load the package locally:

devtools::load_all()

Generating the packaged data from HEAD

To generate the data from the version of this package on github, you can run the following in R:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
install.packages("devtools")
BiocManager::install()
BiocManager::install("getDEE2")
BiocManager::install("DESeq2")
library(DESeq2)
library(Biobase)
library(SummarizedExperiment)
library(getDEE2)
library(devtools)
devtools::install_github(repo="flaviusb/CellScore")
devtools::install_github(repo="flaviusb/homosapienDEE2CellScore")
library(CellScore)
library(homosapienDEE2CellScore)
buildData(build_tsne=FALSE)

Just getting all the data

There is a helper to download the pregenerated data and format it into a tagged list of SummarizedExperiments. If you already have this library installed, you can use it like so:

the_pregenerated_data <- downloadAllTheData()

flaviusb/homosapienDEE2CellScore documentation built on April 11, 2024, 1:47 p.m.