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cellHTS2

Analysis of cell-based screens - revised version of cellHTS

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("cellHTS2")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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")
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 R Script
Reference Manual PDF

Details

biocViews CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization
Version 2.64.0
In Bioconductor since BioC 2.1 (R-2.6) (16 years)
License Artistic-2.0
Depends R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid
Imports GSEABase, Category, stats4, BiocGenerics
Linking To
Suggests ggplot2
System Requirements
Enhances
URL http://www.dkfz.de/signaling http://www.ebi.ac.uk/huber
See More
Depends On Me imageHTS, staRank
Imports Me gespeR, RNAinteract
Suggests Me bioassayR
Links To Me
Build Report  

Package Archives

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

Source Package cellHTS2_2.64.0.tar.gz
Windows Binary cellHTS2_2.64.0.zip
macOS Binary (x86_64) cellHTS2_2.64.0.tgz
macOS Binary (arm64) cellHTS2_2.64.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cellHTS2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cellHTS2
Bioc Package Browser https://code.bioconductor.org/browse/cellHTS2/
Package Short Url https://bioconductor.org/packages/cellHTS2/
Package Downloads Report Download Stats