recipe bioconductor-screcover

scRecover for imputation of single-cell RNA-seq data

Homepage:

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

License:

GPL

Recipe:

/bioconductor-screcover/meta.yaml

scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.

package bioconductor-screcover

versions:

1.18.0-0,  1.16.0-0,  1.13.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

1.18.0-0,  1.16.0-0,  1.13.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bbmle:

>=1.0.18

depends r-doparallel:

depends r-foreach:

depends r-gamlss:

>=4.4-0

depends r-kernlab:

depends r-mass:

>=7.3-45

depends r-matrix:

>=1.2-14

depends r-penalized:

depends r-preseqr:

>=4.0.0

depends r-pscl:

>=1.4.9

depends r-rsvd:

depends r-saver:

>=1.1.1

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-screcover

and update with::

   mamba update bioconductor-screcover

To create a new environment, run:

mamba create --name myenvname bioconductor-screcover

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-screcover:<tag>

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

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Link to this page

Render an 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/bioconductor-screcover/README.html)