https://github.com/nbenn/singlecellfeatures

https://github.com/nbenn/singlecellfeatures

Last synced: about 2 months ago
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• Host: GitHub
• URL: https://github.com/nbenn/singlecellfeatures
• Owner: nbenn
• Created: 2015-03-24T10:47:02.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2016-06-15T09:13:30.000Z (over 8 years ago)
• Last Synced: 2024-10-24T15:56:43.696Z (3 months ago)
• Language: R
• Size: 81.1 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: readme.md

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README

        
# 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](http://www.infectx.org/about_us/iBRAIN2/) based image analysis workflow and is hosted in an [openBIS](http://www.targetinfectx.ch/about_us/openBIS/) instance.

## Installation

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

```R

install.packages("devtools")

library(devtools)

install_github("nbenn/singleCellFeatures")

```

Alternatively the package can be [downloaded](https://github.com/nbenn/singleCellFeatures/archive/master.zip) and installed manually:

```bash

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.

```R

## 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:

```yaml

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](https://wiki.systemsx.ch/pages/viewpage.action?title=InfectX+Single+Cell+Data+Access&spaceKey=InfectXRTD). 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).