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Use when detecting allele-specific expression (ASE), allelic imbalance, or phased allele counts from RNA-seq data with EAGLE (Empirical Analysis of Allele-Specific Gene Expression). Covers phased VCF
Use with AI
Install the MCP server or CLI to instantly fetch EAGLE documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/eagle
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
2 shared topics • 1 shared operation
IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,
2 shared topics • 1 shared operation
Leafcutter — annotation-free RNA splicing quantification from short-read RNA-seq data. Detects differential intron usage, alternative splicing events, outlier splicing (LeafcutterMD), and splicing QTL
2 shared topics • 1 shared operation
PyDESeq2 — Python implementation of DESeq2 for differential gene expression analysis from bulk RNA-seq count data. Performs size factor normalization, genewise dispersion estimation, Wald tests with B
2 shared topics • 1 shared operation
RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i
2 shared topics • 1 shared operation