{ "_id": "6a1867b0acfb0bcc41dc1087", "Package": "enhancerHomologSearch", "Type": "Package", "Title": "Identification of putative mammalian orthologs to given enhancer", "Version": "1.18.0", "Authors@R": "c(person(given=\"Jianhong\", family=\"Ou\", email=\"jou@morgridge.org\", \nrole=c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-8652-2488\")),\nperson(given=\"Valentina\", family=\"Cigliola\", role=c(\"dtc\")),\nperson(given=\"Kenneth\", family=\"Poss\", role=c(\"fnd\")))", "Description": "Get ENCODE data of enhancer region via H3K4me1 peaks and\nsearch homolog regions for given sequences. The candidates of\nenhancer homolog regions can be filtered by distance to target\nTSS. The top candidates from human and mouse will be aligned to\neach other and then exported as multiple alignments with given\nenhancer.", "BugReports": "https://github.com/jianhong/enhancerHomologSearch/issues", "URL": "https://jianhong.github.io/enhancerHomologSearch", "biocViews": "Sequencing, GeneRegulation, Alignment", "License": "GPL (>= 2)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "make libgsl0-dev libbz2-dev libicu-dev liblzma-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:56:41 UTC", "RemoteUrl": "https://github.com/bioc/enhancerHomologSearch", "RemoteRef": "RELEASE_3_23", "RemoteSha": "c43232e600b646564978733bee2df647e967fa82", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-28 14:46:47 UTC", "User": "root" }, "Author": "Jianhong Ou [aut, cre] (ORCID: ),\nValentina Cigliola [dtc],\nKenneth Poss [fnd]", "Maintainer": "Jianhong Ou ", "MD5sum": "c8f4ca92c8286df9e8704bf9bfab292c", "_user": "bioc-release", "_type": "src", "_file": "enhancerHomologSearch_1.18.0.tar.gz", "_fileid": "4f89b56513a60af207239f85196d813bd5014e3de42d591c429cb524aea635d2", "_filesize": 881270, "_sha256": "4f89b56513a60af207239f85196d813bd5014e3de42d591c429cb524aea635d2", "_created": "2026-05-28T14:46:47.000Z", "_published": "2026-05-28T16:05:04.159Z", "_jobs": [ { "job": 78318330428, "time": 570, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7269364084" }, { "job": 78318330310, "time": 868, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7269463189" }, { "job": 78318330056, "time": 978, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7269553390" }, { "job": 78318329977, "time": 919, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7269485055" }, { "job": 78318330034, "time": 1042, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7269572871" }, { "job": 78318330095, "time": 699, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7270603095" }, { "job": 78318330113, "time": 1590, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7270836726" }, { "job": 78318329964, "time": 856, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7270614404" }, { "job": 78318330020, "time": 1878, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7270949185" }, { "job": 78314198603, "time": 1170, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7269087384" }, { "job": 78318329913, "time": 399, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7269291905" }, { "job": 78318329941, "time": 1355, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7269710189" }, { "job": 78318330101, "time": 1192, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7269637935" }, { "job": 78318330071, "time": 1705, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7269854177" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/enhancerHomologSearch", "_commit": { "id": "c43232e600b646564978733bee2df647e967fa82", "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": 1777381001 }, "_maintainer": { "name": "Jianhong Ou", "email": "jou@morgridge.org", "orcid": "0000-0002-8652-2488" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "motifmatchr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BSgenome.Drerio.UCSC.danRer10", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "BSgenome.Mmusculus.UCSC.mm10", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg38.knownGene", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "TxDb.Mmusculus.UCSC.mm10.knownGene", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "MotifDb", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "TFBSTools", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "generegulation", "alignment", "cpp" ], "_stars": 0, "_contributors": [ { "user": "jianhong", "count": 54, "uuid": 5640707 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 330, "source": "https://www.bioconductor.org/packages/stats/bioc/enhancerHomologSearch" }, "_devurl": "https://github.com/jianhong/enhancerhomologsearch", "_pkgdown": "https://jianhong.github.io/enhancerHomologSearch", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/enhancerHomologSearch.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jianhong/enhancerhomologsearch", "_realowner": "bioc", "_cranurl": false, "_exports": [ "alignment", "alignmentOne", "coerce", "conservedMotifs", "distance", "distance<-", "Enhancers", "genome", "genome<-", "getENCODEdata", "getSeq", "peaks", "peaks<-", "query_tfbp", "queryEncode", "saveAlignments", "searchTFBPS", "seqinfo", "show", "shuffle", "subset", "subsetByOverlaps", "tfbp" ], "_datasets": [ { "name": "motifs", "title": "Pre-clustered motifs from human and mouse", "object": "motifs", "file": "motifs.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "alignment", "title": "Output", "topics": [ "alignment" ] }, { "page": "alignmentOne", "title": "Get alignment scores", "topics": [ "alignmentOne" ] }, { "page": "conservedMotifs", "title": "check the conserved motifs in the orthologs", "topics": [ "conservedMotifs" ] }, { "page": "Enhancers-class", "title": "Class '\"Enhancers\"'", "topics": [ "$,Enhancers-method", "$<-,Enhancers-method", "coerce", "coerce,Enhancers,GRanges-method", "distance", "distance,Enhancers,ANY-method", "distance,Enhancers-method", "distance<-", "distance<-,Enhancers,ANY-method", "distance<-,Enhancers-method", "Enhancers", "Enhancers-class", "genome", "genome,Enhancers-method", "genome<-", "genome<-,Enhancers,BSgenome-method", "genome<-,Enhancers-method", "getSeq,Enhancers-method", "peaks", "peaks,Enhancers-method", "peaks<-", "peaks<-,Enhancers,GRanges-method", "peaks<-,Enhancers-method", "query_tfbp", "query_tfbp,Enhancers,ANY-method", "query_tfbp,Enhancers-method", "seqinfo,Enhancers-method", "show,Enhancers-method", "subset,Enhancers-method", "subsetByOverlaps,Enhancers,ANY-method", "subsetByOverlpas,Enhancers-method", "tfbp", "tfbp,Enhancers,ANY-method", "tfbp,Enhancers-method" ] }, { "page": "getENCODEdata", "title": "Download enhancer sequences from ENCODE", "topics": [ "getENCODEdata" ] }, { "page": "motifs", "title": "Pre-clustered motifs from human and mouse", "topics": [ "motifs" ] }, { "page": "queryEncode", "title": "query data from ENCODE by predefined criteria", "topics": [ "queryEncode" ] }, { "page": "saveAlignments", "title": "output alignments", "topics": [ "saveAlignments" ] }, { "page": "searchTFBPS", "title": "Transcription Factor Binding Pattern Similarity (TFBPS) search", "topics": [ "searchTFBPS" ] }, { "page": "shuffle", "title": "shuffle reads", "topics": [ "shuffle" ] } ], "_readme": "https://github.com/bioc/enhancerHomologSearch/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "caTools", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "DirichletMultinomial", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "gtools", "httr", "httr2", "IRanges", "jsonlite", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "motifmatchr", "openssl", "pillar", "pkgconfig", "purrr", "pwalign", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "seqLogo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "TFBSTools", "TFMPvalue", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XML", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "enhancerHomologSearch.Rmd", "filename": "enhancerHomologSearch.html", "title": "enhancerHomologSearch Guide", "author": "Jianhong Ou", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Step 1, prepare target enhancer sequences.", "Step 2, download candidate regions of enhancers from ENCODE by H3K4me1 marks", "Step 3, get alignment score for target enhancer and candidate enhancers.", "Step 4, filter the candidate regions.", "Step 5, alignment for the enhancer and the orthologs", "Step 6a, for quick evolution enhancers, check the conserved motifs in the orthologs", "Step 6b, for slow evolution enhancers, export the multiple alignments in order.", "Session info" ], "created": "2021-06-21 23:58:46", "modified": "2023-10-25 16:49:55", "commits": 14 } ], "_score": 4.653212513775344, "_indexed": false, "_nocasepkg": "enhancerhomologsearch", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/enhancerHomologSearch", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-05-28T14:56:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "40641a9d51664cdb5191912c8d165209044774f85fabb136e2428021692dcb46", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-05-28T14:59:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "007ae377ca1be73f58098c89decb49ebb0ac98d32b43fd09ba0e46455d6cf7d7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.6.0", "os": "linux", "version": "1.18.0", "date": "2026-05-28T14:56:38.000Z", "distro": "noble", "arch": "aarch64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "c6d064cebf0be5c863d1238385d2fae3a4b01abcc4050cd1ba347c1256c59e10", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.6.0", "os": "linux", "version": "1.18.0", "date": "2026-05-28T14:58:53.000Z", "distro": "noble", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "1e16168b78ea434e07e9c389fe65402eaf123b2bbf519b8ba585acd22d440d43", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-05-28T15:41:53.000Z", "arch": "aarch64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "bab307970faa5d3a7c19a166795be5ec037fcd82567acdc2cd6e38b412211c40", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-05-28T15:41:57.000Z", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "3a990a671fa73adc374e98b93c7a8c04d87a2bb9b78e780aea9843ec59a6baed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.6.0", "os": "mac", "version": "1.18.0", "date": "2026-05-28T15:40:39.000Z", "arch": "aarch64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "74000447b9070c4a95479873f509736b0a741160baeafc7951d755d609a009a3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.6.0", "os": "mac", "version": "1.18.0", "date": "2026-05-28T15:43:25.000Z", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "6d467155bf4324ab20a16c0d35949a85370f2b0680189587a371f6fc1de6d479", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.6.0", "os": "wasm", "version": "1.18.0", "date": "2026-05-28T14:56:08.000Z", "arch": "emscripten", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "b056cbec70f122924fa77320b067e8d3207581acacfb0d46ebcb290f8af4ea42", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.7.0", "os": "win", "version": "1.18.0", "date": "2026-05-28T14:57:04.000Z", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "c404adffd8e48b8fd9d126e26b49072792cd8f0bc8ccb9fca48991dfb423f1c7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.5.3", "os": "win", "version": "1.18.0", "date": "2026-05-28T14:56:55.000Z", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "466cd132ec5ee6df51ffaeaebb00f4e470cad6f1d1c40d3f0f91fdb4fa6bba5d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" }, { "r": "4.6.0", "os": "win", "version": "1.18.0", "date": "2026-05-28T14:56:57.000Z", "arch": "x86_64", "commit": "c43232e600b646564978733bee2df647e967fa82", "fileid": "bd1b421b7608289b5ef2aafdc0eb5b6db5dda2f3e24fced6a957b9fe5e6e4671", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26581123426" } ] }