cellHTS2

DOI: 10.18129/B9.bioc.cellHTS2    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see cellHTS2.

Analysis of cell-based screens - revised version of cellHTS

Bioconductor version: 3.12

This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.

Author: Ligia Bras, Wolfgang Huber <whuber at embl.de>, Michael Boutros <m.boutros at dkfz.de>, Gregoire Pau <gpau at embl.de>, Florian Hahne <florian.hahne at novartis.com>

Maintainer: Joseph Barry <joseph.barry at embl.de>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("cellHTS2")

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("cellHTS2")

 

PDF	R Script	Main vignette (complete version): End-to-end analysis of cell-based screens
PDF	R Script	Main vignette: End-to-end analysis of cell-based screens
PDF	R Script	Supplement: enhancer-suppressor screens
PDF	R Script	Supplement: multi-channel assays
PDF		Reference Manual

Details

biocViews	CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization
Version	2.54.0
In Bioconductor since	BioC 2.1 (R-2.6) (13.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid
Imports	prada, GSEABase, Category, stats4, BiocGenerics
LinkingTo
Suggests	ggplot2
SystemRequirements
Enhances
URL	http://www.dkfz.de/signaling http://www.ebi.ac.uk/huber
Depends On Me	imageHTS, staRank
Imports Me	gespeR, RNAinteract
Suggests Me	bioassayR, prada
Links To Me
Build Report

Package Archives

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

Source Package	cellHTS2_2.54.0.tar.gz
Windows Binary	cellHTS2_2.54.0.zip
macOS 10.13 (High Sierra)	cellHTS2_2.54.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cellHTS2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cellHTS2
Package Short Url	https://bioconductor.org/packages/cellHTS2/
Package Downloads Report	Download Stats