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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cellHTS2")
In most cases, you don't need to download the package archive at all.
cellHTS2
Analysis of cell-based screens - revised version of cellHTS
Bioconductor version: 2.14
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cellHTS2")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cellHTS2")
| R Script | 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 | |
| Reference Manual |
Details
| biocViews | CellBasedAssays, Preprocessing, Software, Visualization |
| Version | 2.28.0 |
| In Bioconductor since | BioC 2.1 (R-2.6) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid |
| Imports | prada, GSEABase, Category, stats4 |
| Suggests | |
| System Requirements | |
| URL | http://www.dkfz.de/signaling http://www.ebi.ac.uk/huber |
| Depends On Me | coRNAi, imageHTS, staRank |
| Imports Me | HTSanalyzeR, RNAinteract |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cellHTS2_2.28.0.tar.gz |
| Windows Binary | cellHTS2_2.28.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | cellHTS2_2.28.0.tgz |
| Mac OS X 10.9 (Mavericks) | cellHTS2_2.28.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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