tLOH

tLOH assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data by calculating Bayes factors at likely heterozygous single-nucleotide polymorphism (SNP) positions.

Key Features:

• Bayes factor calculation: Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event.
• Allele fraction visualization: A plotting function visualizes allele fraction per chromosome.
• Aggregated Bayes factor visualization: A plotting function visualizes aggregated Bayes factor per chromosome.
• VCF input support: The tool requires spatial transcriptomics cluster and allele count information at likely heterozygous SNP positions in VCF format with required fields allele depth (AD) with counts for reference/alternative alleles and read depth (DP).
• 10X Genomics Visium compatibility: 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.

Scientific Applications:

• Loss of heterozygosity detection: tLOH assesses evidence for loss of heterozygosity (LOH) in spatial transcriptomics data at the cluster level.
• Spatial transcriptomics analysis: The tool enables investigation of LOH events in spatially resolved transcriptomics data from the 10X Genomics Visium Spatial Gene Expression platform.

Methodology:

Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event.