{ "_id": "6a1aeca31d7bb097a09f4a18", "Package": "tLOH", "Version": "1.20.0", "Type": "Package", "Date": "2021-05-5", "Title": "Assessment of evidence for LOH in spatial transcriptomics\npre-processed data using Bayes factor calculations", "Authors@R": "c(\nperson(\"Michelle\", \"Webb\", email=\"michelgw@usc.edu\",role=c(\"cre\",\"aut\")),\nperson(\"David\",\"Craig\",email=\"davidwcr@usc.edu\", role=c(\"aut\"))\n)", "Description": "tLOH, or transcriptomicsLOH, assesses evidence for loss of\nheterozygosity (LOH) in pre-processed spatial transcriptomics\ndata. This tool requires spatial transcriptomics cluster and\nallele count information at likely heterozygous\nsingle-nucleotide polymorphism (SNP) positions in VCF format.\nBayes factors are calculated at each SNP to determine\nlikelihood of potential loss of heterozygosity event. Two\nplotting functions are included to visualize allele fraction\nand aggregated Bayes factor per chromosome. Data generated with\nthe 10X Genomics Visium Spatial Gene Expression platform must\nbe pre-processed to obtain an individual sample VCF with\ncolumns for each cluster. Required fields are allele depth (AD)\nwith counts for reference/alternative alleles and read depth\n(DP).", "License": "MIT + file LICENSE", "URL": "https://github.com/USCDTG/tLOH", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "BugReports": "https://github.com/USCDTG/tLOH/issues", "biocViews": "CopyNumberVariation, Transcription, SNP, GeneExpression,\nTranscriptomics", "RoxygenNote": "7.2.1", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:55:52 UTC", "RemoteUrl": "https://github.com/bioc/tLOH", "RemoteRef": "RELEASE_3_23", "RemoteSha": "d2ec0cce884394d40dbc883f2f27b1d6dd6732b9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:41:44 UTC", "User": "root" }, "Author": "Michelle Webb [cre, aut],\nDavid Craig [aut]", "Maintainer": "Michelle Webb ", "MD5sum": 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even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380952 }, "_maintainer": { "name": "Michelle Webb", "email": "michelgw@usc.edu", "login": "michelgw", "description": "", "uuid": 31837356 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "scales", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "MatrixGenerics", "role": "Imports" }, { "package": "bestNormalize", "role": "Imports" }, { "package": "depmixS4", "role": "Imports" }, { "package": "naniar", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "knitr", 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