synlet

DOI: 10.18129/B9.bioc.synlet    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see synlet.

Hits Selection for Synthetic Lethal RNAi Screen Data

Bioconductor version: 3.8

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 at dkfz.de>

Maintainer: Chunxuan Shao <c.shao at dkfz.de>

Installation

To install this package, start R (version "3.5") and enter:

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

 

HTML	R Script	A working Demo for synlet
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, FeatureExtraction, ImmunoOncology, Preprocessing, QualityControl, Software, Visualization
Version	1.12.1
In Bioconductor since	BioC 3.2 (R-3.2) (3.5 years)
License	GPL-3
Depends	R (>= 3.2.0), ggplot2
Imports	doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2
LinkingTo
Suggests	knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	synlet_1.12.1.tar.gz
Windows Binary	synlet_1.12.1.zip
Mac OS X 10.11 (El Capitan)	synlet_1.12.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/synlet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/synlet
Package Short Url	http://bioconductor.org/packages/synlet/
Package Downloads Report	Download Stats