{ "_id": "6a1ab1cb1d7bb097a09d5a4e", "Package": "pram", "Title": "Pooling RNA-seq datasets for assembling transcript models", "Version": "1.29.0", "Authors@R": "c(\nperson( given=\"Peng\", family=\"Liu\",\nemail = \"pliu55.wisc+bioconductor@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson( given=\"Colin N.\", family=\"Dewey\", role = c(\"aut\")),\nperson( given=\"Sündüz\", family=\"Keleş\", role = c(\"aut\")) )", "Description": "Publicly available RNA-seq data is routinely used for\nretrospective analysis to elucidate new biology. Novel\ntranscript discovery enabled by large collections of RNA-seq\ndatasets has emerged as one of such analysis. To increase the\npower of transcript discovery from large collections of RNA-seq\ndatasets, we developed a new R package named Pooling RNA-seq\nand Assembling Models (PRAM), which builds transcript models in\nintergenic regions from pooled RNA-seq datasets. This package\nincludes functions for defining intergenic regions, extracting\nand pooling related RNA-seq alignments, predicting, selected,\nand evaluating transcript models.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "URL": "https://github.com/pliu55/pram", "BugReports": "https://github.com/pliu55/pram/issues", "RoxygenNote": "6.1.0", "Collate": "'Param.R' 'Transcript.R' 'buildModel.R' 'defIgRanges.R'\n'evalModel.R' 'prepIgBam.R' 'runPRAM.R' 'selModel.R' 'util.R'", "VignetteBuilder": "knitr", "biocViews": "Software, Technology, Sequencing, RNASeq,\nBiologicalQuestion, GenePrediction, GenomeAnnotation,\nResearchField, Transcriptomics", "SystemsRequirements": "buildModel() and runPRAM() functions require\nexternal software Cufflinks, StringTie, and/or TACO. For\ndetails, please see the 'Required external software' section in\nvignette's 'Building transcript models: buildModel()'.", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:43 UTC", "RemoteUrl": "https://github.com/bioc/pram", "RemoteRef": "HEAD", "RemoteSha": "e06acb573ce9114023f0f6012dc671a8aa8cbd73", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:07:04 UTC", "User": "root" }, "Author": "Peng Liu [aut, cre],\nColin N. Dewey [aut],\nSündüz Keleş [aut]", "Maintainer": "Peng Liu ", "MD5sum": "62c5e332e1804c7efcb488e2c2b8766f", "_user": "bioc", "_type": "src", "_file": "pram_1.29.0.tar.gz", "_fileid": "2e6cdde680d123cfaf7d829cd1bc8f6dc7e11349c68759e7e9afe8947bd3aed3", "_filesize": 2908453, "_sha256": "2e6cdde680d123cfaf7d829cd1bc8f6dc7e11349c68759e7e9afe8947bd3aed3", "_created": "2026-05-30T07:07:04.000Z", "_published": "2026-05-30T09:45:47.087Z", "_jobs": [ { "job": 78632400031, "time": 189, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306348650" }, { "job": 78632400009, "time": 372, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306369627" }, { "job": 78632400005, "time": 385, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306371199" }, { "job": 78632400033, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307212768" }, { "job": 78632400020, "time": 184, "config": 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