{ "_id": "6abcdd9599f7aa8c6aa4d391", "Package": "primirTSS", "Title": "Prediction of pri-miRNA Transcription Start Site", "Version": "1.31.0", "Author": "Pumin Li [aut, cre], Qi Xu [aut], Jie Li [aut], Jin Wang [aut]", "Maintainer": "Pumin Li ", "Description": "A fast, convenient tool to identify the TSSs of miRNAs by\nintegrating the data of H3K4me3 and Pol II as well as combining\nthe conservation level and sequence feature, provided within\nboth command-line and graphical interfaces, which achieves a\nbetter performance than the previous non-cell-specific methods\non miRNA TSSs.", "License": "GPL-2", "Encoding": "UTF-8", "RoxygenNote": "7.1.0", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, Sequencing, RNASeq, Genetics, Preprocessing,\nTranscription, GeneRegulation", "URL": "https://github.com/ipumin/primirTSS", "BugReports": "http://github.com/ipumin/primirTSS/issues", "Config/pak/sysreqs": "cmake make libgsl0-dev libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:38 UTC", "RemoteUrl": "https://github.com/bioc/primirTSS", "RemoteRef": "HEAD", "RemoteSha": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-30 09:28:52 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "primirTSS_1.31.0.tar.gz", "_fileid": "https://r2.ropensci.org/1ab6821a6ce45e5db92d6dfd8952ffeb2ee2b35eb1520ff4536a52ff39824f22", "_filesize": 3954588, "_sha256": "1ab6821a6ce45e5db92d6dfd8952ffeb2ee2b35eb1520ff4536a52ff39824f22", "_expires": "2027-01-08T09:59:47.000Z", "_created": "2026-09-30T09:28:52.000Z", "_published": "2026-09-30T09:59:49.874Z", "_bioccheck": { "error": 1, "warning": 0, "note": 14 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940", "_status": "success", "_upstream": "https://github.com/bioc/primirTSS", "_commit": { "id": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380518 }, "_maintainer": { "name": "Pumin Li", "email": "ipumin@163.com", "login": "ipumin", "description": "", "uuid": 41713540 }, "_distro": "resolute", "_jobs": [ { "job": 109825543691, "time": 347, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11087744574" }, { "job": 109825543414, "time": 541, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11088351258" }, { "job": 109825543431, "time": 680, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11087754479" }, { "job": 109825543382, "time": 356, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11089308017" }, { "job": 109825543467, "time": 329, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11089333070" }, { "job": 109822928106, "time": 451, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11087373253" }, { "job": 109825543498, "time": 263, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11087558685" }, { "job": 109825543460, "time": 378, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11088118948" }, { "job": 109825543392, "time": 383, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11088258385" }, { "job": 109825543447, "time": 385, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11087583903" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.32.2", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.18.2", "role": "Imports" }, { "package": "rtracklayer", "version": ">= 1.40.3", "role": "Imports" }, { "package": "dplyr", "version": ">= 0.7.6", "role": "Imports" }, { "package": "stringr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "tidyr", "version": ">= 0.8.1", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.48.0", "role": "Imports" }, { "package": "purrr", "version": ">= 0.2.5", "role": "Imports" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "version": ">= 1.4.1", "role": "Imports" }, { "package": "phastCons100way.UCSC.hg38", "version": ">= 3.7.1", "role": "Imports" }, { "package": "GenomicScores", "version": ">= 1.4.1", "role": "Imports" }, { "package": "shiny", "version": ">= 1.0.5", "role": "Imports" }, { "package": "Gviz", "version": ">= 1.24.0", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.26.0", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.14.10", "role": "Imports" }, { "package": "TFBSTools", "version": ">= 1.18.0", "role": "Imports" }, { "package": "JASPAR2018", "version": ">= 1.1.1", "role": "Imports" }, { "package": "tibble", "version": ">= 1.4.2", "role": "Imports" }, { "package": "R.utils", "version": ">= 2.6.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "rnaseq", "genetics", "preprocessing", "transcription", "generegulation" ], "_stars": 0, "_contributors": [ { "user": "ipumin", "count": 43, "uuid": 41713540 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 470, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 534, "source": "https://www.bioconductor.org/packages/stats/bioc/primirTSS" }, "_devurl": "https://github.com/ipumin/primirtss", "_searchresults": 0, "_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/primirTSS.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/ipumin/primirtss", "_realowner": "bioc", "_cranurl": false, "_exports": [ "find_tss", "peak_join", "peak_merge", "plot_primiRNA", "run_primirTSSapp", "trans_cor" ], "_help": [ { "page": "find_tss", "title": "Predict TSSs of miRNA", "topics": [ "find_tss" ] }, { "page": "peak_join", "title": "Integrate H3K4me3 data and Pol II data.", "topics": [ "peak_join" ] }, { "page": "peak_merge", "title": "Merge adjacent peaks within H3K4me3 or Pol II data.", "topics": [ "peak_merge" ] }, { "page": "plot_primiRNA", "title": "Plot the result of prediction for miRNA", "topics": [ "plot_primiRNA" ] }, { "page": "primirTSS", "title": "primirTSS: Search for putative TSSs of miRNA", "topics": [ "primirTSS" ] }, { "page": "run_primirTSSapp", "title": "Predict TSSs of miRNA using a graphical web interface.", "topics": [ "run_primirTSSapp" ] }, { "page": "trans_cor", "title": "transform one hg coordinates to another", "topics": [ "trans_cor" ] } ], "_readme": "https://github.com/bioc/primirTSS/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocParallel", "BiocVersion", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "BSgenome.Hsapiens.UCSC.hg38", "bslib", "cachem", "caTools", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dir.expiry", "DirichletMultinomial", "dplyr", "ensembldb", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GenomicScores", "ggplot2", "glue", "gridExtra", "gtable", "gtools", "Gviz", "h5mread", "HDF5Array", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "interp", "IRanges", "isoband", "JASPAR2018", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "later", "lattice", "latticeExtra", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "otel", "phastCons100way.UCSC.hg38", "pillar", "pkgconfig", "png", "prettyunits", "progress", "promises", "ProtGenerics", "purrr", "pwalign", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "seqLogo", "shiny", "snow", "sourcetools", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "TFBSTools", "TFMPvalue", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "primirTSS.Rmd", "filename": "primirTSS.html", "title": "primirTSS", "engine": "knitr::rmarkdown", "headings": [ "1 Introduction", "2 Find the best putative TSS", "Installation", "1 primirTSS", "2 Install Java SE Development Kit(JDK)", "3 Load the package into R session", "3 Getting Started", "Step 1: Process of H3K4me3 and Pol II data", "Step 2: Predict most possible TSS for miRNA", "Step 3: Searching for TFs", "Step4: Analysis of results", "4 Plot the prediction of TSS for miRNA", "5 Graphical web interface for prediction", "TAG1: Find the best putative TSS", "TAG2: Plot pri-miRNA TSS", "Session info" ], "created": "2018-07-27 17:34:33", "modified": "2018-09-07 14:52:27", "commits": 12 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "primirtss", "_universes": [ "bioc", "ipumin" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-09-30T09:35:17.000Z", "distro": "resolute", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/dad677b1fc55d552d79f5bca0952e71d8c4fd4e60f2dd914ac0b8c7d3703e172", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-09-30T09:37:56.000Z", "distro": "resolute", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/33350b65ad5968523a2ef62beee0739a75382c702b5f5015bb4e1cbc0219d943", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-09-30T09:55:45.000Z", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/ddf9eee582ba06abdccb6224f988cc317982df05fd7d2be6eaf2c5d72994f5d2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-09-30T09:56:38.000Z", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/f96c76b0ea76b4d5ef96c296faf44863c4ee8c4fb3dbdff769a74965c53745ac", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-09-30T09:34:00.000Z", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/27e37b8a04d1ffba50a20a2f1a0773b151a2e8b9fd7b4140ed5d154f5cdd20e5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-09-30T09:32:22.000Z", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/cff0728bc1bb02d712b8b15777d796f553a080a40bdf3e7f7fc16e2f354a00ad", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-09-30T09:32:36.000Z", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/298d75283612c8555826c2d22a59f1a1cc2e0e42cef7229e34ec0773d54b79fe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-09-30T09:32:39.000Z", "commit": "28597fa8128b537a6f6cba9203d8bbdc2bd4fe59", "fileid": "https://r2.ropensci.org/e4a52470051e890aab068dc53b20e9fcba92a980ee6806371d56081ec39a71d4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695633940" } ] }