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phASER (Phase and Allele Specific Expression from RNA) is a tool for phasing variants and quantifying allele-specific expression (ASE) from RNA-seq data. Use this skill for haplotype phasing with RNA-
Use with AI
Install the MCP server or CLI to instantly fetch phASER documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/phaser
Use when working with ASEQ — Allele-Specific Expression Quantification — an R command-line tool for detecting allelic imbalance from RNA-seq data. Counts reference and alternative allele reads at hete
1 shared topic • 2 shared operations
iClusterPlus — Bioconductor R package for integrative clustering of multi-omics data. Performs joint latent variable modeling of multiple genomic data types (e.g., SNP copy number, methylation, gene e
1 shared topic • 2 shared operations
QuASAR (Quantitative Allele-Specific Analysis of Reads) — R package for detecting allele-specific expression (ASE) and allelic imbalance from RNA-seq data. Uses a beta-binomial model to test for ASE a
1 shared topic • 2 shared operations
SUPPA2 — fast, accurate analysis of alternative splicing from RNA-seq data. Calculates PSI (Percent Spliced In) values per event and per transcript from transcript quantification (Salmon, kallisto, RS
1 shared topic • 2 shared operations
Vireo (vireoSNP) is a Bayesian variational inference tool for donor demultiplexing in pooled single-cell RNA-seq and single-cell ATAC-seq experiments. It assigns cells to donors using SNP genotype inf
1 shared topic • 2 shared operations