Introduction | Load the package and data. | Quality control | Z and Z' factor | Heatmap of screen data | Scatter plot of screen data | Knock-down effect | Hits selection | Student's t-test | Median +- k*MAD | Rank products method | Redundant siRNA activity method | Summary | References
Package: synlet 2.13.0
Chunxuan Shao
synlet: Hits Selection for Synthetic Lethal RNAi Screen Data
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.
Authors:
synlet_2.13.0.tar.gz
synlet_2.13.0.zip(r-4.7)synlet_2.13.0.zip(r-4.6)synlet_2.13.0.zip(r-4.5)
synlet_2.13.0.tgz(r-4.6-any)synlet_2.13.0.tgz(r-4.5-any)
synlet_2.13.0.tar.gz(r-4.7-any)synlet_2.13.0.tar.gz(r-4.6-any)
synlet_2.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
synlet/json (API)
| # Install 'synlet' in R: |
| install.packages('synlet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- example_dt - Synthetic lethal RNAi screen example data.
On BioConductor:synlet-2.13.0(bioc 3.24)synlet-2.12.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologycellbasedassaysqualitycontrolpreprocessingvisualizationfeatureextraction
Last updated from:e414905da8. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 169 | ||
| linux-devel-x86_64 | OK | 179 | ||
| source / vignettes | OK | 208 | ||
| linux-release-x86_64 | OK | 182 | ||
| macos-release-arm64 | OK | 95 | ||
| macos-oldrel-arm64 | OK | 100 | ||
| windows-devel | OK | 96 | ||
| windows-release | OK | 103 | ||
| windows-oldrel | OK | 97 | ||
| wasm-release | OK | 119 |
Exports:bScoremadSelectplateHeatmaprankProdHitsrsaHitsscatterPlotsiRNAPlottTestzFactor
Dependencies:clicpp11data.tablefarverggplot2gluegmpgtableisobandlabelinglifecyclemagrittrpatchworkR6RankProdRColorBrewerrlangRmpfrS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate B-score | bScore |
| Synthetic lethal RNAi screen example data. | example_dt |
| Select hits basing on median +- k*MAD | madSelect |
| Heatmap of all plates | plateHeatmap |
| Select hits by the rank product method | rankProdHits |
| Select hits by RSA | rsaHits |
| Scatter plot of RNAi screen results | scatterPlot |
| Plot siRNA data and quality metrics. | siRNAPlot |
| student's t-test on B-score | tTest |
| Calcualte the Z and Z' factor | zFactor |