synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

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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.

Author
Chunxuan Shao <c.shao@dkfz.de>
Date of publication
None
Maintainer
Chunxuan Shao <c.shao@dkfz.de>
License
GPL-3
Version
1.4.0

View on Bioconductor

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

Files in this package

synlet/DESCRIPTION
synlet/NAMESPACE
synlet/NEWS
synlet/R
synlet/R/bScore.R
synlet/R/exampleDat.R
synlet/R/madSelect.R
synlet/R/normFuncs.R
synlet/R/plateHeatmap.R
synlet/R/rankProdHits.R
synlet/R/rsaHits.R
synlet/R/scatterPlot.R
synlet/R/siRNAPlot.R
synlet/R/tTest.R
synlet/R/zFactor.R
synlet/build
synlet/build/vignette.rds
synlet/data
synlet/data/exampleDat.rda
synlet/inst
synlet/inst/doc
synlet/inst/doc/synlet-vignette.R
synlet/inst/doc/synlet-vignette.Rmd
synlet/inst/doc/synlet-vignette.html
synlet/man
synlet/man/bScore.Rd
synlet/man/exampleDat.Rd
synlet/man/madSelect.Rd
synlet/man/plateHeatmap.Rd
synlet/man/rankProdHits.Rd
synlet/man/rsaHits.Rd
synlet/man/scatterPlot.Rd
synlet/man/siRNAPlot.Rd
synlet/man/tTest.Rd
synlet/man/zFactor.Rd
synlet/tests
synlet/tests/testthat
synlet/tests/testthat.R
synlet/tests/testthat/test-bScore.R
synlet/tests/testthat/test-mad.R
synlet/tests/testthat/test-zFactor.R
synlet/vignettes
synlet/vignettes/AAK1.png
synlet/vignettes/synlet-vignette.Rmd