{ "_id": "6a194fbbacfb0bcc41ddf15b", "Package": "PhIPData", "Type": "Package", "Title": "Container for PhIP-Seq Experiments", "Version": "1.20.0", "Authors@R": "c(person(\"Athena\", \"Chen\", email = \"achen70@jhu.edu\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-6900-2264\")),\nperson(\"Rob\", \"Scharpf\", email = \"rscharpf@jhu.edu\",\nrole = c(\"aut\")),\nperson(\"Ingo\", \"Ruczinski\", email = \"ingo@jhu.edu\",\nrole = c(\"aut\")))", "Description": "PhIPData defines an S4 class for phage-immunoprecipitation\nsequencing (PhIP-seq) experiments. Buliding upon the\nRangedSummarizedExperiment class, PhIPData enables users to\ncoordinate metadata with experimental data in analyses.\nAdditionally, PhIPData provides specialized methods to subset\nand identify beads-only samples, subset objects using virus\naliases, and use existing peptide libraries to populate object\nparameters.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Infrastructure, DataRepresentation, Sequencing, Coverage", "BugReports": "https://github.com/athchen/PhIPData/issues", "Collate": "'defineBeads.R' 'PhIPData-class.R' 'alias.R' 'library.R'\n'subset.R' 'summaries.R' 'zzz.R'", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:55:10 UTC", "RemoteUrl": "https://github.com/bioc/PhIPData", "RemoteRef": "RELEASE_3_23", "RemoteSha": "89046875da3584626b7e92bc775ed626f87a598e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:27:33 UTC", "User": "root" }, "Author": "Athena Chen [aut, cre] (ORCID: ),\nRob Scharpf [aut],\nIngo Ruczinski [aut]", "Maintainer": "Athena Chen ", "MD5sum": "124d557dac65c5fc4d7e6525186487f9", "_user": "bioc-release", "_type": "src", "_file": "PhIPData_1.20.0.tar.gz", "_fileid": "9ab6435614dd0636d43bdf577d4cb2d21725523c5cd3625af5f6897eabc4ee45", "_filesize": 746901, "_sha256": "9ab6435614dd0636d43bdf577d4cb2d21725523c5cd3625af5f6897eabc4ee45", "_created": "2026-05-29T07:27:33.000Z", "_published": "2026-05-29T08:35:07.865Z", "_jobs": [ { "job": 78457169751, "time": 179, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285444508" }, { "job": 78457169742, "time": 325, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7285486586" }, { "job": 78457169815, "time": 312, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7285483273" }, { "job": 78457169799, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7286536461" }, { "job": 78457169750, "time": 174, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7286525923" }, { "job": 78456617850, "time": 240, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285388292" }, { "job": 78457169757, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285429334" }, { "job": 78457169780, "time": 243, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7285462884" }, { "job": 78457169733, "time": 269, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7285470410" }, { "job": 78457169873, "time": 278, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7285473442" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PhIPData", "_commit": { "id": "89046875da3584626b7e92bc775ed626f87a598e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380910 }, "_maintainer": { "name": "Athena Chen", "email": "achen70@jhu.edu", "login": "athchen", "description": "data scientist and statistician at Gate Biosciences. Recent PhD graduate from the department of biostatistics at Johns Hopkins SPH", "uuid": 10517467, "orcid": "0000-0001-6900-2264" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "SummarizedExperiment", "version": ">= 1.3.81", "role": "Depends" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "datarepresentation", "sequencing", "coverage" ], "_stars": 7, "_contributors": [ { "user": "athchen", "count": 91, "uuid": 10517467 }, { "user": "nturaga", "count": 4, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 332, "source": "https://www.bioconductor.org/packages/stats/bioc/PhIPData" }, "_devurl": "https://github.com/athchen/phipdata", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PhIPData.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/athchen/phipdata", "_realowner": "bioc", "_cranurl": false, "_exports": [ "assay<-", "assays<-", "counts", "counts<-", "deleteAlias", "getAlias", "getBeadsName", "getLibrary", "librarySize", "listLibrary", "logfc", "logfc<-", "makeLibrary", "peptideInfo", "peptideInfo<-", "PhIPData", "prob", "prob<-", "propReads", "removeLibrary", "sampleInfo", "sampleInfo<-", "setAlias", "setBeadsName", "subsetBeads" ], "_help": [ { "page": "aliases", "title": "Using aliases to subset virus data", "topics": [ "aliases", "deleteAlias", "getAlias", "setAlias" ] }, { "page": "defineBeads", "title": "Defining how beads-only samples are encoded.", "topics": [ "defineBeads", "getBeadsName", "setBeadsName" ] }, { "page": "librarySize", "title": "Calculate total read counts for each sample.", "topics": [ "librarySize" ] }, { "page": "peptideLibraries", "title": "Peptide libraries", "topics": [ "getLibrary", "listLibrary", "makeLibrary", "peptideLibraries", "removeLibrary" ] }, { "page": "PhIPData-class", "title": "The PhIPData class", "topics": [ ".PhIPData", "PhIPData", "PhIPData-class" ] }, { "page": "PhIPData-methods", "title": "Accessing and Modifying Information in PhIPData objects", "topics": [ "assay<-,PhIPData,character-method", "assay<-,PhIPData,missing-method", "assay<-,PhIPData,numeric-method", "assays<-,PhIPData,list-method", "assays<-,PhIPData,SimpleList-method", "counts,PhIPData-method", "counts<-,PhIPData-method", "logfc", "logfc,PhIPData-method", "logfc<-", "logfc<-,PhIPData-method", "peptideInfo", "peptideInfo,PhIPData-method", "peptideInfo<-", "peptideInfo<-,PhIPData-method", "PhIPData-methods", "prob", "prob,PhIPData-method", "prob<-", "prob<-,PhIPData-method", "sampleInfo", "sampleInfo,PhIPData-method", "sampleInfo<-", "sampleInfo<-,PhIPData-method" ] }, { "page": "propReads", "title": "Proportion of sample reads", "topics": [ "propReads" ] }, { "page": "subsetBeads", "title": "Subset beads-only samples", "topics": [ "subsetBeads" ] } ], "_readme": "https://github.com/bioc/PhIPData/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "edgeR", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "lattice", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "PhIPData.Rmd", "filename": "PhIPData.html", "title": "PhIPData: A Container for PhIP-Seq Experiments", "author": "Athena Chen, Rob Scharpf, and Ingo Ruczinski", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction", "Components of a PhIPData Object", "Accessing and modifying components of PhIPData object", "Assays", "Peptide metadata", "Sample metadata", "Experimental metadata", "Common operations on PhIPData objects", "Subsetting", "PhIPData summaries", "Using template libraries", "Using aliases", "Coercion from PhIPData to other containers", "sessionInfo()" ], "created": "2021-01-06 16:31:04", "modified": "2022-02-05 02:12:15", "commits": 12 } ], "_score": 5.3222192947339195, "_indexed": false, "_nocasepkg": "phipdata", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/PhIPData", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:31:04.000Z", "distro": "noble", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "d0e71e3921ca16cf83e330991d5cc06bea0cd6165f055814ffc1e7fbff6dd9f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:30:53.000Z", "distro": "noble", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "98bc872807766e2a4d5a0e156094155f6185db312811b3e142b040c2fd533dd5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-05-29T08:32:49.000Z", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "0fe0c731be6e24f74b3dfe3b9019ac64689e33daf29e16383d4ab00af2770ed5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-05-29T08:32:29.000Z", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "b266faeff1825e3587e621a2151508359e94ede77e9288e8f25d498d32337e79", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-05-29T07:30:24.000Z", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "bfd25af12f46229b45e4d34906bd138f3f3e7c46f8e995c540e42a64fec36f1f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:29:31.000Z", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "ebcb54291d2b6ef5f6be5049bed0bf16e79a12f617244e722410ac12954da6e9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:29:12.000Z", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "9c362b88d64f21f1a4f94b3208418f12f2de86c892c26dc914580046a9b8263c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:29:15.000Z", "commit": "89046875da3584626b7e92bc775ed626f87a598e", "fileid": "526b17a35fbfa9a159463c2efbbf71f98b5569941df9f836fdd772cf7b80dc3d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624092129" } ] }