recipe bioconductor-spiky

Spike-in calibration for cell-free MeDIP

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-spiky/meta.yaml

spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.

package bioconductor-spiky

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• 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-s4vectors >=0.36.0,<0.37.0

• r-bamlss

• r-base >=4.2,<4.3.0a0

• r-blandaltmanleh

• r-ggplot2

• r-scales

Required By:

Installation

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

conda install bioconductor-spiky

and update with:

conda update bioconductor-spiky

or use the docker container:

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

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

Download stats

Link to this page

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