Package: easier 1.11.0

Oscar Lapuente-Santana

easier: Estimate Systems Immune Response from RNA-seq data

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

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easier/json (API)
NEWS

# Install 'easier' in R:
install.packages('easier', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:easier-1.11.0(bioc 3.20)easier-1.10.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

12 exports 0.82 score 163 dependencies

Last updated 2 months agofrom:c08b7ee333

Exports:assess_immune_responsecategorize_TMBcompute_CC_pairscompute_CCpair_scorecompute_cell_fractionscompute_LR_pairscompute_pathway_activitycompute_scores_immune_responsecompute_TF_activityexplore_biomarkerspredict_immune_responseretrieve_easier_score

Dependencies:abindAnnotationDbiAnnotationHubaskpassbackportsbcellViperBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbootbriobroomcachemcallrcarcarDatacaToolsclicodetoolscoincolorspacecorrplotcowplotcpp11crayoncurlDBIdbplyrdecoupleRDelayedArraydescDESeq2diffobjdigestdorotheadplyreasierDataevaluateExperimentHubfansifarverfastmapfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegplotsgridExtragtablegtoolshttrIRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelibcoinlifecyclelimSolvelme4locfitlpSolvemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodeltoolsmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslparallellypbkrtestpillarpkgbuildpkgconfigpkgloadplogrplyrpngpolynompraisepreprocessCoreprocessxprogenypspurrrquadprogquantiseqrquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrematch2reshape2rlangROCRrprojrootRSQLiterstatixS4ArraysS4VectorssandwichscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystestthatTH.datatibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewaldowithrXVectoryamlzlibbioczoo

easier User Manual <right>![](easier_logo.png){#id .class width=60 height=60}

Oscar Lapuente-Santana, Federico Marini, Arsenij Ustjanzew, Francesca Finotello, Federica Eduati

Rendered fromeasier_user_manual.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2023-07-06
Started: 2021-10-01

Readme and manuals

Help Manual

Help pageTopics
Assess easier score as predictor of patients' immune responseassess_immune_response
Perform matrix Z-score normalizationcalc_z_score
Define tumor mutational burden (TMB) categories.categorize_TMB
Compute Expanded Immune signature (Ayers_expIS) scorecompute_Ayers_expIS
Compute cell-cell interactions scores using computed ligand-receptor weightscompute_CC_pairs
Compute cell-cell pair scorecompute_CCpair_score
Compute immune cell fractions from gene expression using quanTIseqcompute_cell_fractions
Compute chemokine signature (chemokines) scorecompute_chemokines
Compute cytolytic activity (CYT) scorecompute_CYT
Compute Davoli immune signature (Davoli_IS) scorecompute_Davoli_IS
Compute IFNy signature (IFNy) scorecompute_IFNy
Compute Immuno-Predictive Score (IMPRES) and Micro Satellite Instability (MSI) status scorecompute_IMPRES_MSI
Compute ligand-receptor pair weights from TPM bulk gene expressioncompute_LR_pairs
Compute pathway activity from gene expression using PROGENycompute_pathway_activity
Compute three scores from the immune resistance program: resF_down (RIR), resF_up, resF (resF_up - resF_down)compute_RIR
Compute Roh immune score (Roh_IS)compute_Roh_IS
Compute published scores of immune responsecompute_scores_immune_response
Compute T cell-inflamed signature (Tcell_inflamed) scorecompute_Tcell_inflamed
Compute transcription factor activity from gene expression using DoRothEAcompute_TF_activity
Computation of tertiary lymphoid structures signature (TLS) scorecompute_TLS
Converts a continuous variable into categoricaldiscretize
easier: predicting immune response by using quantitative descriptors of the tumor microenvironment extracted from RNA-seq data.easier-pkg
Explore biomarkers of immune responseexplore_biomarkers
Compute overall expression (OE) of the immune resistance program used in the computation of repressed immune resistance signature (RIR) score.get_OE_bulk
Compute random scores of the immune resistance program used in the computation of repressed immune resistance signature (RIR) score.get_semi_random_OE
Compute predicted immune responsepredict_immune_response
Predict single-view immune responsepredict_with_rmtlr
Gene re-annotation using HGNC symbolsreannotate_genes
Retrieve easier scores of immune responseretrieve_easier_score
Regularized Multi-Task Linear Regression (RMTLR) model predictionsrmtlr_test