apeglm

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

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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

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Salmon is an ultrafast, bias-correcting tool for quantifying transcript abundances from RNA-seq reads using quasi-mapping or selective alignment. Alevin is Salmon's single-cell mode for generating cel

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sleuth — R package for differential expression analysis of RNA-seq data at the transcript level. Works with kallisto bootstrap quantifications to model technical variability using a response error mod

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sva — R/Bioconductor package for surrogate variable analysis, batch effect correction, and unwanted variation removal in high-throughput experiments. Provides sva() for estimating surrogate variables,

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