- 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:
- 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
- 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-seq2pathway/README.html)