InfectX Kinome Publication

Below you can download the supporting data sets. Please pick the suitable format (from Microsoft Excel, Open Document or Tab Separated Text), depending on the software you want to use. User name and password is given in the InfectX paper "Simultaneous analysis of large-scale RNAi screens for pathogen entry", in chapter "Availability of supporting data".
Microscope images can be accessed through the web-link in the column "OpenBIS_Link" in the raw data table.

Download Supplements in Microsoft Excel Format:

InfectXKinomeData-RawData.xls Data tables, see RawData-Description.pdf
InfectXKinomeData-InputPMM.xls Input for PMM.R, see InputPMM-Description.pdf
InfectXKinomeData-OutputPMM.xls Results of PMM.R, see OutputPMM-Description.pdf

Download Supplements in Open Document Format:

InfectXKinomeData-RawData.ods Data tables, see RawData-Description.pdf
InfectXKinomeData-InputPMM.ods Input for PMM.R, see InputPMM-Description.pdf
InfectXKinomeData-OutputPMM.ods Results of PMM.R, see OutputPMM-Description.pdf

Download Supplements in Tab Separated Text Format:

InfectXKinomeData-RawData.csv Data tables, see RawData-Description.pdf
InfectXKinomeData-InputPMM.csv Input for PMM.R, see InputPMM-Description.pdf
InfectXKinomeData-OutputPMM.csv Results of PMM.R, see OutputPMM-Description.pdf

Download R-package for Parallel Mixed Model:

The Parallel Mixed Model page Now available on Bioconductor


gespeR - Gene Specific Phenotype Estimator

Description

gespeR estimates gene-specific phenotypes from off-target confounded RNAi screens. Observed phenotype for a specfic siRNA is modeled as a linear combination of gene-specific phenotypes from the on- and all off-target genes. gespeR is hosted on GitHub and available through Bioconductor. The package is released under the GNU General Public License (GPL) version 3 and includes examples and a vignette.

Target Relation Matrices

Wrapper scripts to run TargetScan in batch mode for the prediction of siRNA-to-gene target relation matrices are available on GitHub, including a README with step-by-step instructions. Pre-computed siRNA-to-gene target relation matrices for libraries used within the InfectX consortium are stored in .rds files using R's serialization interface for single objects. Load the data in R using the function readRDS(). Note that loading target relation matrices can require up to 5GB of RAM.

Pathogen Infection Screen Phenotypes

High-content, image based phenotypes for pathogen infection RNAi screens from the InfectX consortium are hosted at PubChem. Step-by-step instructions in form of a R/Vignette demonstrating how to download, pre-process and deconvolute pathogen infection screen phnotypes can be found at https://www1.ethz.ch/bsse/cbg/software/gespeR/Deconvolute_Pathogen_Screens.