recipe bioconductor-ccimpute

ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-ccimpute/meta.yaml

Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.

package bioconductor-ccimpute

versions:

1.4.0-0,  1.2.1-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-simlr:

>=1.28.0,<1.29.0

depends bioconductor-simlr:

>=1.28.0,<1.29.0a0

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-matrixstats:

depends r-rcpp:

depends r-rcppeigen:

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-ccimpute

and update with::

   mamba update bioconductor-ccimpute

To create a new environment, run:

mamba create --name myenvname bioconductor-ccimpute

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-ccimpute:<tag>

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

Download stats

Link to this page

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