rnaiscreen: A pan-viral perturbation dataset

In cbg-ethz/knockdown: Statistical Analysis of High-Throughput Genetic Perturbation Screens

Description

Example PerturbationData object consisting of several integrated viral RNAi screens.

Usage

data(rnaiscreen)

Format

A PerturbationData object containing a tibble with 16 columns, each describing a feature.

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

Poenisch, Marion, et al. (2015), Identification of HNRNPK as Regulator of Hepatitis C Virus Particle Production.
PLoS Pathogens

Cortese, Mirko, et al. (2019), Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus Replication and Virion Production.
Cell Reports

• 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

Examples

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

cbg-ethz/knockdown documentation built on Feb. 11, 2020, 6:25 p.m.