recipe bioconductor-easier

Estimate Systems Immune Response from RNA-seq data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-easier/meta.yaml

This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.

package bioconductor-easier

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-dorothea >=1.10.0,<1.11.0

• bioconductor-easierdata >=1.4.0,<1.5.0

• bioconductor-progeny >=1.20.0,<1.21.0

• bioconductor-quantiseqr >=1.6.0,<1.7.0

• r-base >=4.2,<4.3.0a0

• r-coin

• r-dplyr

• r-ggplot2

• r-ggpubr

• r-ggrepel

• r-matrixstats

• r-reshape2

• r-rlang

• r-rocr

• r-rstatix

Required By:

Installation

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

conda install bioconductor-easier

and update with:

conda update bioconductor-easier

or use the docker container:

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

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

Download stats

Link to this page

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