SUPPA2

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

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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

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DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

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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

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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-

1 shared topic • 2 shared operations