recipe bioconductor-seq2pathway

a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/seq2pathway.html

License:

GPL-2

Recipe:

/bioconductor-seq2pathway/meta.yaml

Links:

biotools: seq2pathway

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.

package bioconductor-seq2pathway

Versions:

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-1,  1.14.0-1, 

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-1,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0

Depends:

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-seq2pathway.data >=1.30.0,<1.31.0

• r-base >=4.2,<4.3.0a0

• r-gsa

• r-nnet

• r-wgcna

Required By:

Installation

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

conda install bioconductor-seq2pathway

and update with:

conda update bioconductor-seq2pathway

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-seq2pathway:<tag>

(see bioconductor-seq2pathway/tags for valid values for <tag>)

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