Jti

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

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Corset — C++ tool for clustering de novo assembled transcripts into gene-level groups and producing gene-level counts for differential expression analysis. Groups contigs from Trinity, Trans-ABySS, or

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EnhancedVolcano — R/Bioconductor package for creating publication-ready volcano plots with enhanced colouring and labeling from differential expression results. Visualize DESeq2, limma, edgeR output w

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scVelo — RNA velocity generalized through dynamical modeling. Estimates splicing kinetics from single-cell RNA-seq data using steady-state, stochastic, and dynamical models to infer cellular dynamics,

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Velocyto — RNA velocity estimation tool that distinguishes unspliced and spliced mRNAs in single-cell RNA-seq data to predict future cell states. Provides a CLI for counting spliced/unspliced/ambiguou

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