nbenn/infx: OpenBIS API Access to the InfectX Data Repository

The Open Source Biology Information System (openBIS) is a general purpose framework for management, annotation and publication of large data sets that arise from biological experiments. By making the JSON-RPC based openBIS API available to R, image-based high throughput screening data as generated by the InfectX/TargetInfectX projects can be browsed, searched and downloaded directly from R. Currently, several kinome-wide RNA interference screens performed on HeLa cells in presence of a selection of bacterial and viral pathogens and using oligo libraries form multiple vendors are available. Further genome-wide screens are forthcoming. The full data obtained from these experiments is accessible, including raw microscopy images, object segmentation masks, single cell feature data generated by CellProfiler and infection scoring data, alongside rich meta data and quality control data.

Getting started

Package details

Maintainer
LicenseGPL-3 | file LICENSE
Version0.1.0
URL https://ropensci.github.io/infx http://www.infectx.ch https://www.targetinfectx.ch https://labnotebook.ch
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("nbenn/infx")
nbenn/infx documentation built on Oct. 7, 2018, 5:12 p.m.