cellHTS2

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see cellHTS2.

Analysis of cell-based screens - revised version of cellHTS

Bioconductor version: 3.18

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization

Version 2.66.0

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

URL http://www.dkfz.de/signaling http://www.ebi.ac.uk/huber

Suggests ggplot2

Linking To

Enhances

Depends On Me imageHTS, 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_2.66.0.tar.gz

Windows Binary cellHTS2_2.66.0.zip (64-bit only)

macOS Binary (x86_64) cellHTS2_2.66.0.tgz

macOS Binary (arm64) cellHTS2_2.66.0.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/

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