recipe bioconductor-ipath

iPath pipeline for detecting perturbed pathways at individual level






iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes.

package bioconductor-ipath

(downloads) docker_bioconductor-ipath



depends bioconductor-biocparallel:


depends bioconductor-biocparallel:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-ggplot2:

depends r-ggpubr:

depends r-matrixstats:

depends r-mclust:

depends r-rcpp:


depends r-rcpparmadillo:

depends r-survival:

depends r-survminer:



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-ipath

and update with::

   mamba update bioconductor-ipath

To create a new environment, run:

mamba create --name myenvname bioconductor-ipath

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<tag>

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

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