recipe bioconductor-simlr

Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SIMLR.html

License:

file LICENSE

Recipe:

/bioconductor-simlr/meta.yaml

Links:

biotools: simlr, doi: 10.1101/118901

Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.

package bioconductor-simlr

versions:

1.28.0-0,  1.26.1-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1, 

1.28.0-0,  1.26.1-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-0,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

depends r-pracma:

depends r-rcpp:

depends r-rcppannoy:

depends r-rspectra:

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-simlr

and update with::

   mamba update bioconductor-simlr

To create a new environment, run:

mamba create --name myenvname bioconductor-simlr

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-simlr:<tag>

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

Download stats

Link to this page

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