recipe bioconductor-gviz

Plotting data and annotation information along genomic coordinates

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/Gviz.html

License:

Artistic-2.0

Recipe:

/bioconductor-gviz/meta.yaml

Links:

biotools: gviz

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

package bioconductor-gviz

Versions:

1.42.0-0,  1.38.0-0,  1.36.1-0,  1.34.1-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.26.4-0, 

1.42.0-0,  1.38.0-0,  1.36.1-0,  1.34.1-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.26.4-0,  1.24.0-0,  1.22.3-0,  1.22.0-0,  1.20.0-0,  1.16.5-2,  1.14.2-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-biovizbase >=1.46.0,<1.47.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-ensembldb >=2.22.0,<2.23.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-xvector >=0.38.0,<0.39.0

• r-base >=4.2,<4.3.0a0

• r-digest >=0.6.8

• r-lattice

• r-latticeextra >=0.6-26

• r-matrixstats >=0.8.14

• r-rcolorbrewer

Required By:

• bioconductor-primirtss

• bioconductor-variantfiltering

• bioconductor-regutools

• r-shaman

• bioconductor-pviz

• bioconductor-stan

• bioconductor-epimutacions

• bioconductor-rnamodr

• bioconductor-ping

• bioconductor-genomicinteractions

• bioconductor-methylpipe

• bioconductor-srnadiff

• bioconductor-ogre

• bioconductor-splinter

• clinker

• bioconductor-mcsea

• bioconductor-aspli

• hmftools-linx

• bioconductor-allelicimbalance

• bioconductor-bindingsitefinder

• bioconductor-extrachips

• bioconductor-rnamodr.alkanilineseq

• bioconductor-meal

• bioconductor-cicero

• bioconductor-comet

• bioconductor-cagefightr

• bioconductor-chimeraviz

• bioconductor-dmrcatedata

• bioconductor-genestructuretools

• bioconductor-trackviewer

• bioconductor-aspediafi

• bioconductor-crisprviz

• bioconductor-elmer

• bioconductor-maser

• bioconductor-motifbreakr

• bioconductor-dmrcate

• bioconductor-comapr

• bioconductor-dmrforpairs

• bioconductor-uncoverapplib

• bioconductor-cummerbund

• bioconductor-rnamodr.ribomethseq

• bioconductor-biomvrcns

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-gviz

and update with:

conda update bioconductor-gviz

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-gviz:<tag>

(see bioconductor-gviz/tags for valid values for <tag>)

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