recipe bioconductor-genomicplot

Plot profiles of next generation sequencing data in genomic features

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-genomicplot/meta.yaml

Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.

package bioconductor-genomicplot

versions:

1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-genomation:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-plyranges:

>=1.22.0,<1.23.0

depends bioconductor-rcas:

>=1.28.0,<1.29.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-cowplot:

>=1.1.1

depends r-dplyr:

depends r-ggplot2:

>=3.3.5

depends r-ggplotify:

depends r-ggpubr:

depends r-ggsci:

>=2.9

depends r-ggsignif:

>=0.6.3

depends r-scales:

>=1.2.0

depends r-tidyr:

depends r-venndiagram:

depends r-viridis:

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-genomicplot

and update with::

   mamba update bioconductor-genomicplot

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicplot

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-genomicplot:<tag>

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

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