- recipe bioconductor-cellhts2
Analysis of cell-based screens - revised version of cellHTS
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.
- package bioconductor-cellhts2¶
- depends bioconductor-biobase:
- depends bioconductor-biocgenerics:
- depends bioconductor-category:
- depends bioconductor-genefilter:
- depends bioconductor-gseabase:
- depends bioconductor-splots:
- depends bioconductor-vsn:
- depends r-base:
- depends r-hwriter:
- depends r-locfit:
- depends r-rcolorbrewer:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-cellhts2 and update with:: mamba update bioconductor-cellhts2
To create a new environment, run:
mamba create --name myenvname bioconductor-cellhts2
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-cellhts2:<tag> (see `bioconductor-cellhts2/tags`_ for valid values for ``<tag>``)