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 (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews CopyNumberVariation, GeneExpression, SNP, Software, Transcription, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics
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_1.2.0.tar.gz
Windows Binary tLOH_1.2.0.zip
macOS 10.13 (High Sierra) tLOH_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tLOH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tLOH
Package Short Url https://bioconductor.org/packages/tLOH/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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