synlet: Hits Selection for Synthetic Lethal RNAi Screen Data
Version 1.6.0

Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

Browse man pages Browse package API and functions Browse package files

AuthorChunxuan Shao <c.shao@dkfz.de>
Bioconductor views CellBasedAssays FeatureExtraction Preprocessing QualityControl Visualization
Date of publicationNone
MaintainerChunxuan Shao <c.shao@dkfz.de>
LicenseGPL-3
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("synlet")

Man pages

bScore: Calculate B-score
exampleDat: Synthetic lethal RNAi screen example data.
madSelect: Select hits basing on median +- k*MAD
plateHeatmap: Heatmap of all plates
rankProdHits: Select hits by the rank product method
rsaHits: Select hits by RSA
scatterPlot: Scatter plot of RNAi screen results
siRNAPlot: Plot siRNA data and quality metrics.
tTest: student's t-test basing on B-score
zFactor: Calcualte the Z and Z' factor

Functions

OPI Source code
OPIScore Source code
bScore Man page Source code
exampleDat Man page
ff_bscorePlate Source code
ff_contsiRNANorm Source code
ff_masterPlateValue Source code
ff_plateNorm Source code
ff_ratio_madS Source code
ff_ratio_rsa Source code
ff_rsaRatio Source code
ff_ttest Source code
ff_z Source code
handleOneGroup Source code
madSelect Man page Source code
plateHeatmap Man page Source code
rankProdHits Man page Source code
rsaHits Man page Source code
scatterPlot Man page Source code
siRNAPlot Man page Source code
tTest Man page Source code
zFactor Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/bScore.R
R/exampleDat.R
R/madSelect.R
R/normFuncs.R
R/plateHeatmap.R
R/rankProdHits.R
R/rsaHits.R
R/scatterPlot.R
R/siRNAPlot.R
R/tTest.R
R/zFactor.R
build
build/vignette.rds
data
data/exampleDat.rda
inst
inst/doc
inst/doc/synlet-vignette.R
inst/doc/synlet-vignette.Rmd
inst/doc/synlet-vignette.html
man
man/bScore.Rd
man/exampleDat.Rd
man/madSelect.Rd
man/plateHeatmap.Rd
man/rankProdHits.Rd
man/rsaHits.Rd
man/scatterPlot.Rd
man/siRNAPlot.Rd
man/tTest.Rd
man/zFactor.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-bScore.R
tests/testthat/test-mad.R
tests/testthat/test-zFactor.R
vignettes
vignettes/AAK1.png
vignettes/synlet-vignette.Rmd
synlet documentation built on May 20, 2017, 10:15 p.m.