{ "_id": "6ad5d0b04a34890ab4938d19", "Package": "target", "Type": "Package", "Title": "Predict Combined Function of Transcription Factors", "Version": "1.27.0", "Authors@R": "person(\"Mahmoud\", \"Ahmed\",\nemail = \"mahmoud.s.fahmy@students.kasralainy.edu.eg\",\nrole = c(\"aut\", \"cre\"))", "Description": "Implement the BETA algorithm for infering direct target\ngenes from DNA-binding and perturbation expression data Wang et\nal. (2013) . Extend the algorithm\nto predict the combined function of two DNA-binding elements\nfrom comprable binding and expression data.", "URL": "https://github.com/MahShaaban/target", "BugReports": "https://github.com/MahShaaban/target/issues", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "6.1.1", "biocViews": "Software, StatisticalMethod, Transcription", "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:10 UTC", "RemoteUrl": "https://github.com/bioc/target", "RemoteRef": "HEAD", "RemoteSha": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-19 08:05:12 UTC", "User": "root" }, "Author": "Mahmoud Ahmed [aut, cre]", "Maintainer": "Mahmoud Ahmed ", "_user": "bioc", "_type": "src", "_file": "target_1.27.0.tar.gz", "_fileid": "https://r2.ropensci.org/c3c614b0d618e364dcd4fee3d3f90fb3ede055ff8c878eaa3a9d2fe52499918d", "_filesize": 3660998, "_sha256": "c3c614b0d618e364dcd4fee3d3f90fb3ede055ff8c878eaa3a9d2fe52499918d", "_expires": "2027-01-27T08:11:26.000Z", "_created": "2026-10-19T08:05:12.000Z", "_published": "2026-10-19T08:11:28.768Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_upstream": "https://github.com/bioc/target", "_commit": { "id": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380670 }, "_maintainer": { "name": "Mahmoud Ahmed", "email": "mahmoud.s.fahmy@students.kasralainy.edu.eg", "login": "mahshaaban", "description": "Postdoc", "uuid": 16605756 }, "_distro": "resolute", "_jobs": [ { "job": 117953848442, "time": 146, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12170944663" }, { "job": 117953848602, "time": 326, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12170774619" }, { "job": 117953848659, "time": 249, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12171527224" }, { "job": 117953848527, "time": 119, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12171009851" }, { "job": 117953848534, "time": 119, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12170659690" }, { "job": 117952373696, "time": 235, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12171656082" }, { "job": 117953848583, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12171386548" }, { "job": 117953848641, "time": 120, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12171925480" }, { "job": 117953848675, "time": 121, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12171144290" }, { "job": 117953848505, "time": 108, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12171646395" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shinytest", "role": "Suggests" }, { "package": "shinyBS", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "statisticalmethod", "transcription", "algorithm", "chip-seq", "dna-binding", "gene-regulation", "transcription-factors" ], "_stars": 5, "_contributors": [ { "user": "mahshaaban", "count": 24, "uuid": 16605756 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 478, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 526, "source": "https://www.bioconductor.org/packages/stats/bioc/target" }, "_mentions": 6, "_devurl": "https://github.com/mahshaaban/target", "_searchresults": 2444, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/target.html" ], "_homeurl": "https://github.com/mahshaaban/target", "_realowner": "bioc", "_cranurl": false, "_exports": [ "associated_peaks", "direct_targets", "find_distance", "merge_ranges", "plot_predictions", "rank_product", "score_peaks", "score_regions", "target_app", "test_predictions" ], "_datasets": [ { "name": "real_peaks", "title": "AR peaks in LNCaP cell line", "object": "real_peaks", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "real_transcripts", "title": "Differential expression of DHT treated LNCaP cell line", "object": "real_transcripts", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "sim_peaks", "title": "Simulated peaks", "object": "sim_peaks", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "sim_transcripts", "title": "Simulated transcripts The transcripts chromosome 1 of the mm10 mouse genome with randomly singed statistics assigned to each.", "object": "sim_transcripts", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "associated_peaks", "title": "Predict associated peaks", "topics": [ "associated_peaks" ] }, { "page": "direct_targets", "title": "Predict direct targets", "topics": [ "direct_targets" ] }, { "page": "find_distance", "title": "Find the distance between peaks and regions", "topics": [ "find_distance" ] }, { "page": "merge_ranges", "title": "Merge peaks and regions GRanges", "topics": [ "merge_ranges" ] }, { "page": "plot_predictions", "title": "Plot the ECDF of ranks by groups", "topics": [ "plot_predictions" ] }, { "page": "rank_product", "title": "Calculate the regions rank products", "topics": [ "rank_product" ] }, { "page": "real_peaks", "title": "AR peaks in LNCaP cell line", "topics": [ "real_peaks" ] }, { "page": "real_transcripts", "title": "Differential expression of DHT treated LNCaP cell line", "topics": [ "real_transcripts" ] }, { "page": "score_peaks", "title": "Calculate peak scores", "topics": [ "score_peaks" ] }, { "page": "score_regions", "title": "Calculate region scores", "topics": [ "score_regions" ] }, { "page": "sim_peaks", "title": "Simulated peaks", "topics": [ "sim_peaks" ] }, { "page": "sim_transcripts", "title": "Simulated transcripts The transcripts chromosome 1 of the mm10 mouse genome with randomly singed statistics assigned to each.", "topics": [ "sim_transcripts" ] }, { "page": "target", "title": "'target': Predict Combined Function of Transcription Factors.", "topics": [ "target-package", "target" ] }, { "page": "target_app", "title": "Run the shiny App", "topics": [ "target_app" ] }, { "page": "test_predictions", "title": "Test the ECDF ranks of groups are from same distribution", "topics": [ "test_predictions" ] } ], "_readme": "https://github.com/bioc/target/raw/HEAD/README.md", "_rundeps": [ "base64enc", "BiocGenerics", "bslib", "cachem", "cli", "commonmark", "digest", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "glue", "htmltools", "httpuv", "IRanges", "jquerylib", "jsonlite", "later", "lifecycle", "magrittr", "matrixStats", "memoise", "mime", "otel", "promises", "R6", "rappdirs", "Rcpp", "rlang", "S4Vectors", "sass", "Seqinfo", "shiny", "sourcetools", "withr", "xtable" ], "_vignettes": [ { "source": "extend-target.Rmd", "filename": "extend-target.html", "title": "Using target to predict combined binding", "author": "Mahmoud Ahmed", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Theory", "Example", "Cooperative factors example", "Competitive factors example", "References" ], "created": "2019-08-28 05:36:20", "modified": "2019-09-26 12:07:03", "commits": 3 }, { "source": "target.Rmd", "filename": "target.html", "title": "Using the target package", "author": "Mahmoud Ahmed", "engine": "knitr::rmarkdown", "headings": [ "Overview", "The theory", "Python implementation", "R implementation", "Example", "Advantages of the R implementation", "References" ], "created": "2019-08-28 05:36:20", "modified": "2019-08-28 05:36:20", "commits": 1 } ], "_score": 8.16625245195416, "_indexed": true, "_nocasepkg": "target", "_universes": [ "bioc", "mahshaaban" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-10-19T08:10:01.000Z", "distro": "resolute", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/b4ebe854fd72ae2e1a525aa0ad24eacb5c37f01eafbe9a3025b04e3d35874c9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.6.1", "os": "linux", "version": "1.27.0", "date": "2026-10-19T08:08:52.000Z", "distro": "resolute", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/aeb8827f756bd2c4e929c500cd2b016a542b2e53cc3ca0037ffeff7759025c56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-10-19T08:08:47.000Z", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/cdcc5714becd7f51c674cc08292bcd8ef3f63bcbb34da309a0a0405b3099280b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.6.1", "os": "mac", "version": "1.27.0", "date": "2026-10-19T08:08:02.000Z", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/d79a7dcd653107d46df7a1a25719cddab93ad4527aa3fc9a84684cf4c0923bf9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-10-19T08:07:18.000Z", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/b8fc583e33f17b94acf94ad39a9969f1f9f1dd929f6f5578e2a7b6fbd7ddf8ca", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-10-19T08:06:46.000Z", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/7d5bdaf0fbe92b2cc13327556f392863fc2ecbff8de921c3d52ff33251d5e66b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-10-19T08:06:40.000Z", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/1aa8e811215d14c9a5e788c37fef211a4c083599cf9c7cd3a3a6bde2a1f593c6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" }, { "r": "4.6.1", "os": "win", "version": "1.27.0", "date": "2026-10-19T08:06:43.000Z", "commit": "c38bdfe0e28c49e363ac734e4e24d6ab10f4d356", "fileid": "https://r2.ropensci.org/aff6b0acbbaaaf781ee266bae7a21491852ed3a5352f5ffe097e6b009c180909", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39219826355" } ] }