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synlet

This is the development version of synlet; for the stable release version, see synlet.

Hits Selection for Synthetic Lethal RNAi Screen Data


Bioconductor version: Development (3.19)

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 [aut, cre]

Maintainer: Chunxuan Shao <chunxuan at outlook.com>

Citation (from within R, enter citation("synlet")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("synlet")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("synlet")
A working Demo for synlet HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, FeatureExtraction, ImmunoOncology, Preprocessing, QualityControl, Software, Visualization
Version 2.3.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.5.0)
Imports data.table, ggplot2, grDevices, magrittr, methods, patchwork, RankProd, RColorBrewer, stats, utils
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Suggests BiocStyle, knitr, testthat, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package synlet_2.3.0.tar.gz
Windows Binary synlet_2.3.0.zip
macOS Binary (x86_64) synlet_2.3.0.tgz
macOS Binary (arm64) synlet_2.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/synlet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/synlet
Bioc Package Browser https://code.bioconductor.org/browse/synlet/
Package Short Url https://bioconductor.org/packages/synlet/
Package Downloads Report Download Stats