recipe r-jackstraw

Test for association between the observed data and their systematic patterns of variations. Systematic patterns may be captured by latent variables using principal component analysis (PCA), factor analysis (FA), and related methods. The jackstraw enables statistical testing for association between observed variables and latent variables, as captured by PCs or other estimates. Similarly, unsupervised clustering, such as K-means clustering, partition around medoids (PAM), and others, finds subpopulations among the observed variables. The jackstraw estimates statistical significance of cluster membership, including unsupervised evaluation of cell identities in single cell RNA-seq. P-values and posterior probabilities allows one to rigorously evaluate the strength of cluster membership assignments.

Homepage:

https://CRAN.R-project.org/package=jackstraw

License:

GPL2 / GPL-2.0-only

Recipe:

/r-jackstraw/meta.yaml

package r-jackstraw

(downloads) docker_r-jackstraw

versions:
1.3.9-0,  1.3.8-1,  1.3.8-0,  1.3.1-1,  1.3.1-0,  1.3-6,  1.3-5,  1.3-4,  1.3-3, 

1.3.9-0,  1.3.8-1,  1.3.8-0,  1.3.1-1,  1.3.1-0,  1.3-6,  1.3-5,  1.3-4,  1.3-3,  1.3-2,  1.3-1,  1.3-0

depends bioconductor-qvalue:

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-clusterr:

depends r-corpcor:

depends r-irlba:

depends r-rsvd:

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 r-jackstraw

and update with::

   mamba update r-jackstraw

To create a new environment, run:

mamba create --name myenvname r-jackstraw

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/r-jackstraw:<tag>

(see `r-jackstraw/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/r-jackstraw/README.html)