Package: tLOH
Version: 1.6.0
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
git_url: https://git.bioconductor.org/packages/tLOH
git_branch: RELEASE_3_16
git_last_commit: cb1b340
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: no
Packaged: 2022-11-01 23:14:01 UTC; biocbuild
Author: Michelle Webb [cre, aut],
  David Craig [aut]
Maintainer: Michelle Webb <michelgw@usc.edu>
Built: R 4.2.2; ; 2022-11-08 14:41:15 UTC; unix
