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Use when working with ashr (adaptive shrinkage in R) for empirical Bayes shrinkage of effect size estimates in RNA-seq differential expression analysis. ashr fits mixture priors to (betahat, sebetahat
Use with AI
Install the MCP server or CLI to instantly fetch ashr documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/ashr
ballgown -- R/Bioconductor package for flexible isoform-level differential expression analysis of RNA-seq experiments. Works with StringTie output (.ctab files) to test for differential expression at
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Benchmark and compare bioinformatics tools for a given analysis task using published benchmark data (accuracy, runtime, memory), PrecisionFDA and CAMI challenge results, bc7score community metrics, an
1 shared topic • 1 shared operation
EBSeq is an R/Bioconductor package implementing an empirical Bayes hierarchical model for identifying differentially expressed (DE) genes and isoforms in RNA-seq experiments. It supports both two-cond
1 shared topic • 1 shared operation
Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering
1 shared topic • 1 shared operation
TCGAbiolinks for searching, downloading, and analyzing cancer genomics data from the NCI Genomic Data Commons (GDC). Routes tasks for GDCquery/GDCdownload, data preparation with GDCprepare, differenti
1 shared topic • 1 shared operation