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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Analysis of cell-based screens - revised version of cellHTS

Bioconductor version: Release (3.19)

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 <wolfgang.huber at>, Michael Boutros <m.boutros at>, Gregoire Pau, Florian Hahne <florian.hahne at>

Maintainer: Wolfgang Huber <wolfgang.huber at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

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


biocViews CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization
Version 2.68.0
In Bioconductor since BioC 2.1 (R-2.6) (16.5 years)
License Artistic-2.0
Depends R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid
Imports GSEABase, Category, stats4, BiocGenerics
System Requirements
See More
Suggests ggplot2, GO.db
Linking To
Depends On Me staRank
Imports Me gespeR, RNAinteract
Suggests Me bioassayR
Links To Me
Build Report Build Report

Package Archives

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

Source Package cellHTS2_2.68.0.tar.gz
Windows Binary
macOS Binary (x86_64) cellHTS2_2.68.0.tgz
macOS Binary (arm64) cellHTS2_2.68.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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