InfectX Kinome Publication
Below you can download the supporting data sets. Please pick the suitable format
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
gespeR - Gene Specific Phenotype Estimator
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