recipe bioconductor-yapsa

Yet Another Package for Signature Analysis

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-yapsa/meta.yaml

Links:

biotools: yapsa, doi: 10.1038/nmeth.3252

This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

package bioconductor-yapsa

versions:

1.28.0-0,  1.25.0-0,  1.24.0-0,  1.19.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.25.0-0,  1.24.0-0,  1.19.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome.hsapiens.ucsc.hg19:

>=1.4.0,<1.5.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gtrellis:

>=1.34.0,<1.35.0

depends bioconductor-keggrest:

>=1.42.0,<1.43.0

depends bioconductor-somaticsignatures:

>=2.38.0,<2.39.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-corrplot:

depends r-dendextend:

depends r-doparallel:

depends r-dplyr:

depends r-getoptlong:

depends r-ggbeeswarm:

depends r-ggplot2:

depends r-gridextra:

depends r-limsolve:

depends r-magrittr:

depends r-pmcmrplus:

depends r-pracma:

depends r-reshape2:

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-yapsa

and update with::

   mamba update bioconductor-yapsa

To create a new environment, run:

mamba create --name myenvname bioconductor-yapsa

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-yapsa:<tag>

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

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