tLOH

DOI: 10.18129/B9.bioc.tLOH  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	tLOH
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CopyNumberVariation, GeneExpression, SNP, Software, Transcription, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 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
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/USCDTG/tLOH
BugReports	https://github.com/USCDTG/tLOH/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	tLOH_1.6.0.tar.gz
Windows Binary	tLOH_1.6.0.zip
macOS Binary (x86_64)	tLOH_1.6.0.tgz
macOS Binary (arm64)	tLOH_1.6.0.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