recipe bioconductor-profileplyr

Visualization and annotation of read signal over genomic ranges with profileplyr

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-profileplyr/meta.yaml

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

package bioconductor-profileplyr

Versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.3-0,  1.2.0-0,  1.0.1-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-chipseeker >=1.34.0,<1.35.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-enrichedheatmap >=1.27.0,<1.28.0

• bioconductor-genomeinfodb >=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-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-org.mm.eg.db >=3.16.0,<3.17.0

• bioconductor-rgreat >=2.0.0,<2.1.0

• 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-soggi >=1.30.0,<1.31.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.16.0,<3.17.0

• bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0

• bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0

• r-base >=4.2,<4.3.0a0

• r-circlize

• r-dplyr

• r-ggplot2

• r-magrittr

• r-pheatmap

• r-r.utils

• r-rjson

• r-rlang

• r-tidyr

• r-tiff

Required By:

Installation

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

conda install bioconductor-profileplyr

and update with:

conda update bioconductor-profileplyr

or use the docker container:

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

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

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