Introduction | Bioconductor installation | Differential State analysis | Input data | Differential analyses within sub-populations of cells | Handling covariates and batch effects | Visualizing results | Plotting significant results | Session info

Introduction | Bioconductor installation | Devel installation from github | Aligning reads | Gene-transcript matching | DTU pipeline | Preliminary information | Optional (recommended): transcript pre-filtering | Load the data | salmon input | kallisto input | Optional (recommended): infer an informative prior for the precision parameter | Test for DTU | Results in detail | Gene level results | Transcript level results | Inference with 3 or more groups | Inference with 1 group only | Session info | References

Introduction | Bioconductor installation | Questions, issues and citation | Load the package | Key options | Input data | PSM counts vs. intensities | TPMs (optional) | PEP vs. FDR cutoff | Generate SummarizedExperiment object | Input MetaMorpheus data | Peptide-Spectrum Match (PSM) counts | Intensities | Input Percolator data | Input user provided-data | .tsv or data.frame format | SummarizedExperiment format | Input and pre-process data | Inference | Gene Normalization (optional) | Visualizing results | Assessing convergence via traceplots | Session info | OpenMS and Metamorpheus pipeline | MetaMorpheus pipeline | Percolator pipeline | References

Introduction | Conceptual idea | Mathematical details | Bioconductor installation | Questions, issues and citation | Single-cell RNA-seq pipeline | Input data: alignment and quantification with alevin-fry | Load the package | Load the data | Load USA counts | Load equivalence classes (EC) | QC and filtering | Differential testing | Visualizing results | Bulk RNA-seq pipeline | Input data: alignment and quantification with salmon or kallisto | Load US counts | Session info | References