recipe bioconductor-sictools

Find SNV/Indel differences between two bam files with near relationship

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-sictools/meta.yaml

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

package bioconductor-sictools

versions:

1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-2, 

1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends libblas:

>=3.9.0,<4.0a0

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-doparallel:

>=1.0.8

depends r-matrixstats:

>=0.10.0

depends r-plyr:

>=1.8.3

depends r-stringr:

>=0.6.2

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-sictools

and update with::

   mamba update bioconductor-sictools

To create a new environment, run:

mamba create --name myenvname bioconductor-sictools

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-sictools:<tag>

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

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