recipe bioconductor-seqarchr

Identify Different Architectures of Sequence Elements

Homepage:

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

License:

GPL-3 | file LICENSE

Recipe:

/bioconductor-seqarchr/meta.yaml

seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

package bioconductor-seqarchr

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

depends r-cluster:

depends r-cvtools:

>=0.3.2

depends r-fpc:

depends r-ggplot2:

>=3.1.1

depends r-ggseqlogo:

>=0.1

depends r-mass:

depends r-matrix:

depends r-matrixstats:

depends r-prettyunits:

depends r-reshape2:

>=1.4.3

depends r-reticulate:

>=1.22

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-seqarchr

and update with::

   mamba update bioconductor-seqarchr

To create a new environment, run:

mamba create --name myenvname bioconductor-seqarchr

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-seqarchr:<tag>

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

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