synlet
Hits Selection for Synthetic Lethal RNAi Screen Data
Bioconductor version: Release (3.20)
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("synlet")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| A working Demo for synlet | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, FeatureExtraction, ImmunoOncology, Preprocessing, QualityControl, Software, Visualization |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | data.table, ggplot2, grDevices, magrittr, methods, patchwork, RankProd, RColorBrewer, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | synlet_2.6.0.tar.gz |
| Windows Binary (x86_64) | synlet_2.6.0.zip |
| macOS Binary (x86_64) | synlet_2.6.0.tgz |
| macOS Binary (arm64) | synlet_2.5.0.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 |