easier

DOI: 10.18129/B9.bioc.easier  

Estimate Systems Immune Response from RNA-seq data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	easier User Manual
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, Classification, Epigenetics, ExperimentHubSoftware, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, Regression, Software, SystemsBiology, Transcription
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	progeny, easierData, dorothea(>= 1.6.0), quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils, dplyr, matrixStats, rlang, BiocParallel, reshape2, rstatix, ggrepel, coin
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	easier_1.4.0.tar.gz
Windows Binary	easier_1.4.0.zip
macOS Binary (x86_64)	easier_1.4.0.tgz
macOS Binary (arm64)	easier_1.4.0.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/
Package Downloads Report	Download Stats