rnaiscreen: A sample pan-pathogenic perturbation dataset

In perturbatr: Statistical Analysis of High-Throughput Genetic Perturbation Screens

Description

Example PerturbationData object of two integrated viral RNAi screens that consists of a HCV kinome screen and a SARS kinome screen (see references).

Usage

data(rnaiscreen)

Format

A PerturbationData object containing a tibble with 18 columns, each describing a feature.

Author(s)

Simon Dirmeier | Computational Biology Group, ETH ZURICH | [e-mail]

References

de Wilde, Adriaan H., et al. (2015), A kinome-wide small interfering RNA screen identifies proviral and antiviral host factors in severe acute respiratory syndrome coronavirus replication, including double-stranded RNA-activated protein kinase and early secretory pathway proteins.
Journal of virology

Reiss, Simon, et al. (2011), Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.
Cell Host & Microbe

Friedman J., Hastie T., Hoefling H. and Tibshirani R. (2007), Pathwise coordinate optimization.
The Annals of Applied Statistics

• Condition character names of the viruses

• Replicate integer replicate numer

• Plate integer plate index

• RowIdx integer row index of the well on the plate

• ColIdx integer column index of the well on the plate

• GeneSymbol character HugoSymbol of a gene

• Entrez integer entrez ID

• ReadoutType character readout type, such as 'GFP' or 'Luciferase'

• Control integer coding of controls. '-1' for negative control, '1' for positive control, '0' for regular sample

• Library character library type, such as 'Ambion'

• Perturbation character sirna identifier

• Screen character identifier, for example 'Kinome' or 'Genome'

• Cell character cell type, such as 'Huh7.5'

• ScreenType character screen type, such as 'E/R' for entry/replication

• Design character design of the library, e.g. 'pooled'

• Readout numeric readout value, e.g. GFP measurement or read count

• ReadoutClass character class of the readout, such as 'Readout' or 'Viability'

• NumCells integer number of measured cells per well

Examples

 data(rnaiscreen)
 fit <- hm(rnaiscreen)
 pls <- plot(fit)
 pls[[1]]

perturbatr documentation built on Nov. 8, 2020, 5:15 p.m.