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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "easier" in publications use:'
type: software
license: MIT
title: 'easier: Estimate Systems Immune Response from RNA-seq data'
version: 1.11.0
doi: 10.1016/j.patter.2021.100293
abstract: 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.
authors:
- family-names: Lapuente-Santana
  given-names: Oscar
  email: o.lapuente.santana@tue.nl
  orcid: https://orcid.org/0000-0003-1995-8393
- family-names: Marini
  given-names: Federico
  email: marinif@uni-mainz.de
  orcid: https://orcid.org/0000-0003-3252-7758
- family-names: Ustjanzew
  given-names: Arsenij
  email: arsenij.ustjanzew@uni-mainz.de
  orcid: https://orcid.org/0000-0002-1014-4521
- family-names: Finotello
  given-names: Francesca
  email: francesca.finotello@i-med.ac.at
  orcid: https://orcid.org/0000-0003-0712-4658
- family-names: Eduati
  given-names: Federica
  email: f.eduati@tue.nl
  orcid: https://orcid.org/0000-0002-7822-3867
preferred-citation:
  type: article
  title: Interpretable systems biomarkers predict response to immune-checkpoint inhibitors
  authors:
  - family-names: Lapuente-Santana
    given-names: Oscar
    email: o.lapuente.santana@tue.nl
    orcid: https://orcid.org/0000-0003-1995-8393
  - family-names: Genderen
    given-names: Maisa
    name-particle: van
  - family-names: Hilbers
    given-names: Peter A.J.
  - family-names: Finotello
    given-names: Francesca
    email: francesca.finotello@i-med.ac.at
    orcid: https://orcid.org/0000-0003-0712-4658
  - family-names: Eduati
    given-names: Federica
    email: f.eduati@tue.nl
    orcid: https://orcid.org/0000-0002-7822-3867
  journal: Patterns
  year: '2021'
  month: '8'
  publisher:
    name: Elsevier
  volume: '2'
  issue: '8'
  issn: 2666-3899
  doi: 10.1016/j.patter.2021.100293
repository: https://bioc.r-universe.dev
contact:
- family-names: Lapuente-Santana
  given-names: Oscar
  email: o.lapuente.santana@tue.nl
  orcid: https://orcid.org/0000-0003-1995-8393