recipe bioconductor-cellbarcode

Cellular DNA Barcode Analysis toolkit

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/CellBarcode.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-cellbarcode/meta.yaml

This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon sequencing such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.

package bioconductor-cellbarcode

versions:

1.6.0-0,  1.4.0-1,  1.4.0-0,  1.0.0-2,  1.0.0-1,  1.0.0-0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-shortread:

>=1.58.0,<1.59.0

depends bioconductor-zlibbioc:

>=1.46.0,<1.47.0

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-bh:

depends r-ckmeans.1d.dp:

depends r-data.table:

>=1.12.6

depends r-egg:

depends r-ggplot2:

depends r-magrittr:

depends r-plyr:

depends r-rcpp:

>=1.0.5

depends r-seqinr:

depends r-stringr:

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-cellbarcode

and update with::

   mamba update bioconductor-cellbarcode

To create a new environment, run:

mamba create --name myenvname bioconductor-cellbarcode

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-cellbarcode:<tag>

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

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