{ "_id": "6a10c22aacfb0bcc41ccbc47", "Package": "easier", "Title": "Estimate Systems Immune Response from RNA-seq data", "Version": "1.19.0", "Authors@R": "c(\nperson(\ngiven = \"Oscar\", family = \"Lapuente-Santana\", role = c(\"aut\", \"cre\"),\nemail = \"o.lapuente.santana@tue.nl\", comment = c(ORCID = \"0000-0003-1995-8393\")\n),\nperson(\ngiven = \"Federico\", family = \"Marini\", role = \"aut\",\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n),\nperson(\ngiven = \"Arsenij\", family = \"Ustjanzew\", role = \"aut\",\nemail = \"arsenij.ustjanzew@uni-mainz.de\", comment = c(ORCID = \"0000-0002-1014-4521\")\n),\nperson(\ngiven = \"Francesca\", family = \"Finotello\", role = \"aut\",\nemail = \"francesca.finotello@i-med.ac.at\", comment = c(ORCID = \"0000-0003-0712-4658\")\n),\nperson(\ngiven = \"Federica\", family = \"Eduati\", role = \"aut\",\nemail = \"f.eduati@tue.nl\", comment = c(ORCID = \"0000-0002-7822-3867\")\n)\n)", "Description": "This package provides a workflow for the use of EaSIeR\ntool, developed to assess patients' likelihood to respond to\nICB therapies providing just the patients' RNA-seq data as\ninput. We integrate RNA-seq data with different types of prior\nknowledge to extract quantitative descriptors of the tumor\nmicroenvironment from several points of view, including\ncomposition of the immune repertoire, and activity of intra-\nand extra-cellular communications. Then, we use multi-task\nmachine learning trained in TCGA data to identify how these\ndescriptors can simultaneously predict several state-of-the-art\nhallmarks of anti-cancer immune response. In this way we derive\ncancer-specific models and identify cancer-specific systems\nbiomarkers of immune response. These biomarkers have been\nexperimentally validated in the literature and the performance\nof EaSIeR predictions has been validated using independent\ndatasets form four different cancer types with patients treated\nwith anti-PD1 or anti-PDL1 therapy.", "License": "MIT + file LICENSE", "biocViews": "GeneExpression, Software, Transcription, SystemsBiology,\nPathways, GeneSetEnrichment, ImmunoOncology, Epigenetics,\nClassification, BiomedicalInformatics, Regression,\nExperimentHubSoftware", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:29 UTC", "RemoteUrl": "https://github.com/bioc/easier", "RemoteRef": "HEAD", "RemoteSha": "60fe9abbcc3aa334c8e3db78a2bf0cc9742b3cbd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-04-30 17:33:50 UTC", "User": "root" }, "Author": "Oscar Lapuente-Santana [aut, cre] (ORCID:\n),\nFederico Marini [aut] (ORCID: ),\nArsenij Ustjanzew [aut] (ORCID:\n),\nFrancesca Finotello [aut] (ORCID:\n),\nFederica Eduati [aut] (ORCID: )", "Maintainer": "Oscar Lapuente-Santana ", "MD5sum": "5514f7f7db4907d86ad6309ea1f9df2c", "_user": "bioc", "_type": "src", "_file": "easier_1.19.0.tar.gz", "_fileid": "0cf568b7db1f2ecfdd41d1503d14e827c56a6b2e25fe891809f5c605bd24f136", "_filesize": 3654065, "_sha256": "0cf568b7db1f2ecfdd41d1503d14e827c56a6b2e25fe891809f5c605bd24f136", "_created": "2026-04-30T17:33:50.000Z", "_jobs": [ { "job": 77460232040, "time": 325, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "6736524583" }, { "job": 77460232513, "time": 647, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6736625502" }, { "job": 77460232495, "time": 664, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6736631659" }, { "job": 77460232403, "time": 427, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6738714745" }, { "job": 77460232369, "time": 394, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6738704321" }, { "job": 77460231792, "time": 716, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6736366632" }, { "job": 77460231776, "time": 240, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7170072857" }, { "job": 77460232511, "time": 810, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6736673712" }, { "job": 77460232669, "time": 949, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6736722476" }, { "job": 77460232351, "time": 758, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6736661120" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25179445041", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/easier", "_commit": { "id": "60fe9abbcc3aa334c8e3db78a2bf0cc9742b3cbd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381049 }, "_maintainer": { "name": "Oscar Lapuente-Santana", "email": "o.lapuente.santana@tue.nl", "login": "olapuentesantana", "twitter": "@LapuenteSantana", "uuid": 42207933, "orcid": "0000-0003-1995-8393" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "progeny", "role": "Imports" }, { "package": "easierData", "role": "Imports" }, { "package": "dorothea", "version": ">= 1.6.0", "role": "Imports" }, { "package": "decoupleR", "role": "Imports" }, { "package": "quantiseqr", "role": "Imports" }, { "package": "ROCR", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": 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computation of repressed immune resistance signature (RIR) score.", "topics": [ "get_semi_random_OE" ] }, { "page": "predict_immune_response", "title": "Compute predicted immune response", "topics": [ "predict_immune_response" ] }, { "page": "predict_with_rmtlr", "title": "Predict single-view immune response", "topics": [ "predict_with_rmtlr" ] }, { "page": "reannotate_genes", "title": "Gene re-annotation using HGNC symbols", "topics": [ "reannotate_genes" ] }, { "page": "retrieve_easier_score", "title": "Retrieve easier scores of immune response", "topics": [ "retrieve_easier_score" ] }, { "page": "rmtlr_test", "title": "Regularized Multi-Task Linear Regression (RMTLR) model predictions", "topics": [ "rmtlr_test" ] } ], "_readme": "https://github.com/bioc/easier/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "askpass", "backports", "bcellViper", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocParallel", 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cancer patients [@Mariathasan2018]", "Load data from Mariathasan cohort", "Compute hallmarks of immune response", "Compute quantitative descriptors of the TME", "Obtain patients' predictions of immune response", "Evaluate easier predictions using patients' immunotherapy response", "What if I have an immunotherapy dataset where patients' response is not available?", "Retrieve easier scores of immune response", "Interpret response to immunotherapy through systems biomarkers", "Session info", "References" ], "created": "2021-10-01 13:25:22", "modified": "2023-07-06 14:08:57", "commits": 12 } ], "_score": 4.4623979978989565, "_indexed": true, "_nocasepkg": "easier", "_universes": [ "bioc", "olapuentesantana" ], "_failure": { "version": "1.19.0", "commit": { "id": "60fe9abbcc3aa334c8e3db78a2bf0cc9742b3cbd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381049 }, "buildurl": 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