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miRDeep2 — de novo microRNA (miRNA) discovery and quantification from small RNA-seq data. Identifies known and novel miRNAs by mapping collapsed reads to the genome, scoring hairpin structures, and co
Use with AI
Install the MCP server or CLI to instantly fetch miRDeep2 documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/mirdeep2
IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,
3 shared topics • 1 shared operation
BEASTIE (Bayesian Estimation of Allele-Specific Transcription Integrating Expression) — statistical framework for detecting allele-specific expression (ASE) from RNA-seq data. Uses a Bayesian hierarch
2 shared topics • 2 shared operations
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 • 2 shared operations
Use when performing single-cell QTL (sc-eQTL, sc-sQTL) mapping with SAIGE-QTL. SAIGE-QTL extends the SAIGE framework to single-cell RNA-seq data using Poisson mixed models to handle count overdispersi
2 shared topics • 2 shared operations
salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s
2 shared topics • 2 shared operations