{ "_id": "6a1b02001d7bb097a0a00961", "Package": "saseR", "Type": "Package", "Title": "Scalable Aberrant Splicing and Expression Retrieval", "Date": "2023-06-01", "Version": "1.9.0", "Description": "saseR is a highly performant and fast framework for\naberrant expression and splicing analyses. The main functions\nare: \\itemize{ \\item \\code{\\link{BamtoAspliCounts}} - Process\nBAM files to ASpli counts \\item \\code{\\link{convertASpli}} -\nGet gene, bin or junction counts from ASpli\nSummarizedExperiment \\item \\code{\\link{calculateOffsets}} -\nCreate an offsets assays for aberrant expression or splicing\nanalysis \\item \\code{\\link{saseRfindEncodingDim}} - Estimate\nthe optimal number of latent factors to include when estimating\nthe mean expression \\item \\code{\\link{saseRfit}} - Parameter\nestimation of the negative binomial distribution and compute\np-values for aberrant expression and splicing } For information\nupon how to use these functions, check out our vignette at\n\\url{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd}\nand the saseR paper: Segers, A. et al. (2023). Juggling offsets\nunlocks RNA-seq tools for fast scalable differential usage,\naberrant splicing and expression analyses. bioRxiv.\n\\url{https://doi.org/10.1101/2023.06.29.547014}.", "Authors@R": "c(person(\"Alexandre\", \"Segers\", role = c(\"aut\",\"cre\"),\nemail = \"Alexandre.segers@ugent.be\"),\nperson(\"Jeroen\",\"Gilis\", role=\"ctb\",\nemail = \"Jeroen.Gilis@ugent.be\"),\nperson(\"Mattias\",\"Van Heetvelde\", role=\"ctb\",\nemail = \"Mattias.Vanheetvelde@ugent.be\"),\nperson(\"Elfride\",\"De Baere\", role=\"ctb\",\nemail = \"Elfride.Debaere@ugent.be\"),\nperson(\"Lieven\",\"Clement\", role=\"ctb\",\nemail = \"Lieven.Clement@ugent.be\"))", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "URL": "https://github.com/statOmics/saseR,\nhttps://doi.org/10.1101/2023.06.29.547014", "Encoding": "UTF-8", "LazyData": "FALSE", "RoxygenNote": "7.3.2", "biocViews": "DifferentialExpression, DifferentialSplicing, Regression,\nGeneExpression, AlternativeSplicing, RNASeq, Sequencing,\nSoftware", "BugReports": "https://github.com/statOmics/saseR/issues", "Config/pak/sysreqs": "cmake libglpk-dev make 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 13:02:09 UTC", "RemoteUrl": "https://github.com/bioc/saseR", "RemoteRef": "HEAD", "RemoteSha": "6cb29591266486a108020c1a3f966d3533657e85", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:55:31 UTC", "User": "root" }, "Author": "Alexandre Segers [aut, cre],\nJeroen Gilis [ctb],\nMattias Van Heetvelde [ctb],\nElfride De Baere [ctb],\nLieven Clement [ctb]", "Maintainer": "Alexandre Segers ", "MD5sum": "f8154ef07a3d1c09cd45b9d3b1ce124d", "_user": "bioc", "_type": "src", "_file": "saseR_1.9.0.tar.gz", "_fileid": "fde6165067be0f9e6184121f43b67742ef9450d19d84db5fd44b58afc9f180ca", "_filesize": 1167733, "_sha256": 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