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tLOH

This is the development version of tLOH; for the stable release version, see tLOH.

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations


Bioconductor version: Development (3.19)

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).

Author: Michelle Webb [cre, aut], David Craig [aut]

Maintainer: Michelle Webb <michelgw at usc.edu>

Citation (from within R, enter citation("tLOH")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("tLOH")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tLOH")
tLOH HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CopyNumberVariation, GeneExpression, SNP, Software, Transcription, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr
System Requirements
URL https://github.com/USCDTG/tLOH
Bug Reports https://github.com/USCDTG/tLOH/issues
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tLOH_1.11.0.tar.gz
Windows Binary tLOH_1.11.0.zip (64-bit only)
macOS Binary (x86_64) tLOH_1.11.0.tgz
macOS Binary (arm64) tLOH_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tLOH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tLOH
Bioc Package Browser https://code.bioconductor.org/browse/tLOH/
Package Short Url https://bioconductor.org/packages/tLOH/
Package Downloads Report Download Stats