tLOH
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations
Bioconductor version: Release (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("tLOH")):
Installation
To install this package, start R (version "4.4") 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")| tLOH | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CopyNumberVariation, GeneExpression, SNP, Software, Transcription, Transcriptomics |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tLOH_1.12.0.tar.gz |
| Windows Binary (x86_64) | tLOH_1.12.0.zip |
| macOS Binary (x86_64) | tLOH_1.12.0.tgz |
| macOS Binary (arm64) | tLOH_1.12.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |