recipe bioconductor-seqarchrplus

Downstream analyses of promoter sequence architectures and HTML report generation

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-seqarchrplus/meta.yaml

seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.

package bioconductor-seqarchrplus

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-chipseeker:

>=1.38.0,<1.39.0

depends bioconductor-clusterprofiler:

>=4.10.0,<4.11.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-heatmaps:

>=1.26.0,<1.27.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-seqarchr:

>=1.6.0,<1.7.0

depends bioconductor-seqpattern:

>=1.34.0,<1.35.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

depends r-cowplot:

depends r-factoextra:

depends r-ggimage:

depends r-ggplot2:

depends r-gridextra:

depends r-magick:

depends r-rcolorbrewer:

depends r-scales:

requirements:

additional platforms:

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-seqarchrplus

and update with::

   mamba update bioconductor-seqarchrplus

To create a new environment, run:

mamba create --name myenvname bioconductor-seqarchrplus

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-seqarchrplus:<tag>

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

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