recipe bioconductor-hireadsprocessor

Functions to process LM-PCR reads from 454/Illumina data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-hireadsprocessor/meta.yaml

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

package bioconductor-hireadsprocessor

versions:

1.38.0-0,  1.36.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0, 

1.38.0-0,  1.36.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.1-0,  1.18.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-hiannotator:

>=1.36.0,<1.37.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-readxl:

depends r-soniclength:

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-hireadsprocessor

and update with::

   mamba update bioconductor-hireadsprocessor

To create a new environment, run:

mamba create --name myenvname bioconductor-hireadsprocessor

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-hireadsprocessor:<tag>

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

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