recipe bioconductor-bloodcancermultiomics2017

"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/BloodCancerMultiOmics2017.html

License:

LGPL (>= 3)

Recipe:

/bioconductor-bloodcancermultiomics2017/meta.yaml

The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.

package bioconductor-bloodcancermultiomics2017

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-beeswarm:

depends r-devtools:

depends r-dplyr:

depends r-ggdendro:

depends r-ggplot2:

depends r-glmnet:

depends r-gtable:

depends r-ipflasso:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scales:

depends r-survival:

depends r-tibble:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-bloodcancermultiomics2017

and update with::

   mamba update bioconductor-bloodcancermultiomics2017

To create a new environment, run:

mamba create --name myenvname bioconductor-bloodcancermultiomics2017

with myenvname being 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-bloodcancermultiomics2017:<tag>

(see `bioconductor-bloodcancermultiomics2017/tags`_ for valid values for ``<tag>``)

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