{ "_id": "6a1f221cb401979e734207ef", "Package": "VALERIE", "Title": "Visualising Splicing at Single-Cell Resolution", "Version": "1.1.0", "Description": "Alternative splicing produces a variety of different\nprotein products from a given gene. 'VALERIE' enables\nvisualisation of alternative splicing events from\nhigh-throughput single-cell RNA-sequencing experiments.\n'VALERIE' computes percent spliced-in (PSI) values for\nuser-specified genomic coordinates corresponding to alternative\nsplicing events. PSI is the proportion of sequencing reads\nsupporting the included exon/intron as defined by Shiozawa\n(2018) . PSI are inferred from\nsequencing reads data based on specialised infrastructures for\nrepresenting and computing annotated genomic ranges by Lawrence\n(2013) . Computed PSI for\neach single cell are subsequently presented in the form of a\nheatmap implemented using the 'pheatmap' package by Kolde\n(2010) . Board\noverview of the mean PSI difference and associated p-values\nacross different user-defined groups of single cells are\npresented in the form of a line graph using the 'ggplot2'\npackage by Wickham (2007)\n.", "Encoding": "UTF-8", "Author": "Sean Wen", "Maintainer": "Sean Wen ", "License": "GPL-3", "RoxygenNote": "7.0.2", "VignetteBuilder": "knitr", "ByteCompile": "true", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-16 07:09:48 UTC", "User": "root" }, "Config/pak/sysreqs": "libbz2-dev liblzma-dev xz-utils zlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2020-07-10 09:20:13 UTC", "RemoteUrl": "https://github.com/cran/VALERIE", "RemoteRef": "HEAD", "RemoteSha": "1bdf7ed399add8af8367c18bef52f6662571be87", "MD5sum": "7126207591d98a8ea61a827a83ebdcc4", "_user": "cran", "_type": "src", "_file": "VALERIE_1.1.0.tar.gz", "_fileid": "ea7d1b3d12cfc6d22f2571a771fb9b4fc365909dc91c5d1953bc3cffb90ed6cf", "_filesize": 4805645, "_sha256": 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spliced-in (PSI) computation", "topics": [ "ComputePSI" ] }, { "page": "PlotPSI", "title": "Percent spliced-in (PSI) visualization for alternative splicing events", "topics": [ "PlotPSI" ] }, { "page": "PlotPSI.A3SS.MultiGroups", "title": "Percent spliced in (PSI) visualization for alternative 3' splice sites (A3SS)", "topics": [ "PlotPSI.A3SS.MultiGroups" ] }, { "page": "PlotPSI.A3SS.TwoGroups", "title": "Percent spliced in (PSI) visualization for alternative 3' splice sites (A3SS)", "topics": [ "PlotPSI.A3SS.TwoGroups" ] }, { "page": "PlotPSI.A5SS.MultiGroups", "title": "Percent spliced-in (PSI) visualization for alternative 5' splice sites (A5SS)", "topics": [ "PlotPSI.A5SS.MultiGroups" ] }, { "page": "PlotPSI.A5SS.TwoGroups", "title": "Percent spliced-in (PSI) visualization for alternative 5' splice sites (A5SS)", "topics": [ "PlotPSI.A5SS.TwoGroups" ] }, { "page": "PlotPSI.MXE.MultiGroups", "title": "Percent spliced-in (PSI) visualization for mutually exclusive exons (MXE)", "topics": [ "PlotPSI.MXE.MultiGroups" ] }, { "page": "PlotPSI.MXE.TwoGroups", "title": "Percent spliced-in (PSI) visualization for mutually exclusive exons (MXE)", "topics": [ "PlotPSI.MXE.TwoGroups" ] }, { "page": "PlotPSI.RI.MultiGroups", "title": "Percent spliced-in (PSI) visualization for retained introns (RI)", "topics": [ "PlotPSI.RI.MultiGroups" ] }, { "page": "PlotPSI.RI.TwoGroups", "title": "Percent spliced-in (PSI) visualization for retained introns (RI)", "topics": [ "PlotPSI.RI.TwoGroups" ] }, { "page": "PlotPSI.SE.MultiGroups", "title": "Percent spliced-in (PSI) visualization for skipped exons (SE)", "topics": [ "PlotPSI.SE.MultiGroups" ] }, { "page": "PlotPSI.SE.TwoGroups", "title": "Percent spliced-in (PSI) visualization for skipped exons (SE)", "topics": [ "PlotPSI.SE.TwoGroups" ] } ], "_rundeps": [ "abind", "backports", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "boot", "broom", "car", "carData", "cigarillo", "cli", "codetools", 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