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easier

Estimate Systems Immune Response from RNA-seq data


Bioconductor version: Release (3.18)

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.

Author: Oscar Lapuente-Santana [aut, cre] , Federico Marini [aut] , Arsenij Ustjanzew [aut] , Francesca Finotello [aut] , Federica Eduati [aut]

Maintainer: Oscar Lapuente-Santana <o.lapuente.santana at tue.nl>

Citation (from within R, enter citation("easier")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("easier")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("easier")
easier User Manual HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BiomedicalInformatics, Classification, Epigenetics, ExperimentHubSoftware, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, Regression, Software, SystemsBiology, Transcription
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports progeny, easierData, dorothea(>= 1.6.0), decoupleR, quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils, dplyr, tidyr, tibble, matrixStats, rlang, BiocParallel, reshape2, rstatix, ggrepel, magrittr, coin
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Suggests knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper
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Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package easier_1.8.0.tar.gz
Windows Binary easier_1.8.0.zip
macOS Binary (x86_64) easier_1.8.0.tgz
macOS Binary (arm64) easier_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/easier
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/easier
Bioc Package Browser https://code.bioconductor.org/browse/easier/
Package Short Url https://bioconductor.org/packages/easier/
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