readme.md

In nbenn/singleCellFeatures: Analyze single cell features stored in an openBIS instance

singleCellFeatures

This R package serves to acquire and analyse single cell feature data as generated and compiled by TargetInfectX. The data is produced by iBRAIN2 based image analysis workflow and is hosted in an openBIS instance.

Installation

The easiest way is throught the install_github functionality of the devtools package:

install.packages("devtools")
library(devtools)

install_github("nbenn/singleCellFeatures")

Alternatively the package can be downloaded and installed manually:

unzip ~/Downloads/singleCellFeatures-master.zip
R CMD INSTALL --no-multiarch --with-keep.source ~/Downloads/singleCellFeatures-master

Configuration

Some setup dependent information has to be provided, all of which is stored in a yaml file. The default location of this config file is ~/.singleCellFeaturesConfig. This can be changed on a per-session basis using the function configPathSet() of more permanently, using an .Rprofile file.

## if no config file is present, set one up
# set the config file location
configPathSet("path/to/where/you/want/your/config.yaml")
# create a template file
configInit()
# using a text editor, modify this file for your system

## for inter-session persistence, add the following to your .Rprofile
options(singleCellFeatures.configPath = "path/to/your/config.yaml")

The config file has the following structure:

dataStorage:
  dataDir: "/path/to/data/dir"
  metaDir: "/path/to/metadata/dir"
beeDownloader:
  executable: "/path/to/repo/openBIS/Tools/BeeDataSetDownloader"
openBIS:
  username: "user"
  password: "password"
singleCellFeatures:
  sourceDir: "/path/to/source"

The two entries under dataStorage should be located on a volume with a couple of GB of free storage, to be able to hold a couple of plates. A complete plate uses 1-2 GB of storage, so having upwards of 50 GB available is recommended. The two entries under beeDownloader are concerned with BeeDataSetDownloader. More information available here. The final section holds the path to the local source of this package. It is only used to update the databases in /data (see the utilDatabase.R file).

nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.