- recipe bioconductor-seq2pathway
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
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¶
- depends bioconductor-biomart:
- depends bioconductor-genomicranges:
- depends bioconductor-seq2pathway.data:
- depends r-base:
- depends r-gsa:
- depends r-nnet:
- depends r-wgcna:
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-seq2pathway and update with:: mamba update bioconductor-seq2pathway
To create a new environment, run:
mamba create --name myenvname bioconductor-seq2pathway
myenvnamebeing 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-seq2pathway:<tag> (see `bioconductor-seq2pathway/tags`_ for valid values for ``<tag>``)