cellHTS2
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see cellHTS2.
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 embl.org>, Michael Boutros <m.boutros at dkfz.de>, Gregoire Pau, Florian Hahne <florian.hahne at novartis.com>
Maintainer: Wolfgang Huber <wolfgang.huber at embl.org>
citation("cellHTS2")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Main vignette: End-to-end analysis of cell-based screens | R Script | |
| Supplement: enhancer-suppressor screens | R Script | |
| Supplement: multi-channel assays | R Script | |
| Reference Manual |
Details
| biocViews | CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization |
| Version | 2.68.0 |
| In Bioconductor since | BioC 2.1 (R-2.6) (17 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.huber.embl.de |
See More
| Suggests | ggplot2, GO.db |
| Linking To | |
| Enhances | |
| Depends On Me | staRank |
| Imports Me | RNAinteract, gespeR |
| 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 (x86_64) | cellHTS2_2.68.0.zip (64-bit only) |
| macOS Binary (x86_64) | cellHTS2_2.68.0.tgz |
| macOS Binary (arm64) | cellHTS2_2.68.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cellHTS2 |
| Source Repository (Developer Access) | git clone [email protected]:packages/cellHTS2 |
| Package Short Url | https://bioconductor.org/packages/cellHTS2/ |
| Package Downloads Report | Download Stats |