README.md

In xhdouglas/HTScapacity: An R package for analyzing assay capacity in HTS studies

HTScapacity

An R package for analyzing assay capacity in HTS studies

HTScapacity can be installed from github

install.packages("devtools") # If not already installed

devtools::install_github("xhDouglas/HTScapacity")

Data

Related datasets are stored in Excel files in the subdirectory "extdata".

These data may also be obtained through running the following command lines in R after installing HTScapacity

library(HTScapacity)

data("data.mucinHTS", package="HTScapacity")

data("data.CVB3CRISPR", package="HTScapacity")

data("data.hcvHTS", package="HTScapacity")

The mucin RNAi and HCV RNAi screens were published in

Zhang, X. D. et al. The use of strictly standardized mean difference for hit selection in primary RNA interference high-throughput screening experiments. Journal of biomolecular screening 12, 497-509 (2007).

Zhang, X. D. Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-Scale RNAi Research. (Cambridge University Press, 2011).

The CVB3 CRISPR/CAS9 screen was published originally in

Kim, H. S. et al. Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection. Genome Res 28, 859-868 (2018).

The codes for generating the figures and tables in the paper for assay capacity are stored in the subdirectory "Code.main" in the package.

Functions

HTScapacity contains the following major functions.

capacityPlot.homoVAR.fn

capacityPlot.homoVAR.simple.fn

FoldHit.homoVAR.plot.fn

FoldHit.homoVAR.UMVUE.fn

FoldHit0.homoVAR.fn

FoldHit0core.homoVAR.fn

FoldHitC.homoVAR.fn

Paper

Assay capacity: a new concept for assessing and controlling quality in high-throughput screening studies

xhdouglas/HTScapacity documentation built on Dec. 10, 2020, 8:20 p.m.