Package: tLOH
Version: 1.19.0
Type: Package
Date: 2021-05-5
Title: Assessment of evidence for LOH in spatial transcriptomics
        pre-processed data using Bayes factor calculations
Authors@R: c(
    person("Michelle", "Webb", email="michelgw@usc.edu",role=c("cre","aut")),
    person("David","Craig",email="davidwcr@usc.edu", role=c("aut"))
    )
Description: tLOH, or transcriptomicsLOH, assesses evidence for loss of
        heterozygosity (LOH) in pre-processed spatial transcriptomics
        data. This tool requires spatial transcriptomics cluster and
        allele count information at likely heterozygous
        single-nucleotide polymorphism (SNP) positions in VCF format.
        Bayes factors are calculated at each SNP to determine
        likelihood of potential loss of heterozygosity event. Two
        plotting functions are included to visualize allele fraction
        and aggregated Bayes factor per chromosome. Data generated with
        the 10X Genomics Visium Spatial Gene Expression platform must
        be pre-processed to obtain an individual sample VCF with
        columns for each cluster. Required fields are allele depth (AD)
        with counts for reference/alternative alleles and read depth
        (DP).
License: MIT + file LICENSE
URL: https://github.com/USCDTG/tLOH
Encoding: UTF-8
Suggests: knitr, rmarkdown
Depends: R (>= 4.2)
Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr,
        VariantAnnotation, GenomicRanges, MatrixGenerics,
        bestNormalize, depmixS4, naniar, stringr
VignetteBuilder: knitr
BugReports: https://github.com/USCDTG/tLOH/issues
biocViews: CopyNumberVariation, Transcription, SNP, GeneExpression,
        Transcriptomics
RoxygenNote: 7.2.1
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:08:42 UTC
RemoteUrl: https://github.com/bioc/tLOH
RemoteRef: HEAD
RemoteSha: 7e311dfbc7a28dd0778b122e87dba6cebca43516
NeedsCompilation: no
Packaged: 2026-01-23 07:42:46 UTC; root
Author: Michelle Webb [cre, aut],
  David Craig [aut]
Maintainer: Michelle Webb <michelgw@usc.edu>
Built: R 4.6.0; ; 2026-01-23 07:45:09 UTC; windows
