Standard workflow | Quick start | How to get help for DESeq2 | Acknowledgments | Funding | Input data | Why un-normalized counts? | The DESeqDataSet | Transcript abundance files and tximport / tximeta | Tximeta for import with automatic metadata | Count matrix input | htseq-count input | SummarizedExperiment input | Pre-filtering | Note on factor levels | Collapsing technical replicates | About the pasilla dataset | Differential expression analysis | Log fold change shrinkage for visualization and ranking | Speed-up and parallelization thoughts | p-values and adjusted p-values | Independent hypothesis weighting | Exploring and exporting results | MA-plot | Alternative shrinkage estimators | Plot counts | More information on results columns | Rich visualization and reporting of results | Exporting results to CSV files | Multi-factor designs | Data transformations and visualization | Count data transformations | Blind dispersion estimation | Extracting transformed values | Variance stabilizing transformation | Regularized log transformation | Effects of transformations on the variance | Data quality assessment by sample clustering and visualization | Heatmap of the count matrix | Heatmap of the sample-to-sample distances | Principal component plot of the samples | Variations to the standard workflow | Wald test individual steps | Control features for estimating size factors | Contrasts | Interactions | Time-series experiments | Likelihood ratio test | Extended section on shrinkage estimators | Recommendations for single-cell analysis | Approach to count outliers | Dispersion plot and fitting alternatives | Local or mean dispersion fit | Supply a custom dispersion fit | Independent filtering of results | Tests of log2 fold change above or below a threshold | Access to all calculated values | Sample-/gene-dependent normalization factors | "Model matrix not full rank" | Linear combinations | Group-specific condition effects, individuals nested within groups | Levels without samples | Theory behind DESeq2 | The DESeq2 model | Changes compared to DESeq | Methods changes since the 2014 DESeq2 paper | Count outlier detection | Expanded model matrices | Independent filtering and multiple testing | Filtering criteria | Why does it work? | Frequently asked questions | How can I get support for DESeq2? | Why are some p values set to NA? | How can I get unfiltered DESeq2 results? | How do I use VST or rlog data for differential testing? | Why after VST are there still batches in the PCA plot? | Do normalized counts correct for variables in the design? | Can I use DESeq2 to analyze paired samples? | Can DESeq2 model random effects? | If I have multiple groups, should I run all together or split into pairs of groups? | Can I run DESeq2 to contrast the levels of many groups? | Can I use DESeq2 to analyze a dataset without replicates? | How can I include a continuous covariate in the design formula? | I ran a likelihood ratio test, but results() only gives me one comparison. | What are the exact steps performed by DESeq()? | Is there an official Galaxy tool for DESeq2? | I want to benchmark DESeq2 comparing to other DE tools. | I have trouble installing DESeq2 on Ubuntu/Linux... | Session info | References

Introduction | Preparing tximeta input | Running tximeta | How does it work? | Packages used for caching metadata | Pre-computed digests | SummarizedExperiment output | Retrieve the transcript database | Add exons per transcript | Easy summarization to gene-level | Assign ranges by abundance | Add different identifiers | Differential gene expression analysis | Differential transcript expression and usage analysis | Additional metadata slots | Mixed reference transcripts | salmon mixed reference | Importing oarfish data | Errors connecting to a database | What if digest isn't known? | Linked transcriptomes | Clear linkedTxomes | Loading linkedTxome JSON files | Clear linkedTxomes again | alevin details | Other quantifiers | Acknowledgments | Session info | References

The Swish method | Quick start | Macrophage stimulation experiment | Data import | Read in the column data from CSV | Add a column pointing to your files | Read in quants with tximeta | Differential transcript expression | Running Swish at the transcript level | Plotting results | Differential gene expression | Running Swish at the gene level | Plotting gene results | Differential transcript usage | Interaction designs | Condition and secondary covariates | Create and check paired samples | Swish for interaction effects | Plotting interaction results | Allelic expression analysis | Correlation test | alevin scRNA-seq | Further details | Analysis types supported by Swish | Accounting for continuous variables | Structure of tximeta output | Plotting q-values over statistics | Plotting InfRV | Salmon in alignment mode, how to use tximeta | Permutation schemes for interactions | Session information | References

Introduction | Import transcript-level estimates | salmon | salmon with inferential replicates | kallisto | kallisto with TSV files | RSEM | StringTie | alevin | oarfish | Downstream DGE in Bioconductor | 3' tagged RNA-seq | DESeq2 | edgeR | limma-voom | Acknowledgments | Session info | References

Introduction | Quick start | Finding events from transcript sets | Finding events from DTU results | Input data | The find_*() functions | Output format | Finding splicing events | Finding events from transcript sets | Input format | A synthetic exon set | Building the input by partition | Finding events | Finding events after DTU analysis | Jones et al mouse long read dataset | Loading example data | Preprocessing input data | Finding individual events | Finding all events | Upstream DTU methods | Collapsing redundant events | Identifying complex events | Exon ranges input for splicelogic | Using prepare_exons() | Manual construction | Related tools | Session info

Introduction | Quick start | Method overview | Linking transcripts to TSS | Importing allelic counts | Filtering features | Global allelic imbalance | Plotting results | Differential allelic imbalance | Dynamic allelic imbalance | More complex designs | Further questions | Session info | References

Getting help | Introduction | Methods | Simulation | Operation | Quantification and data import | DTU testing | Workflow | Salmon quantification | Importing counts into R/Bioconductor | Transcript-to-gene mapping | Statistical analysis of differential transcript usage | DRIMSeq | stageR following DRIMSeq | Post-hoc filtering on the standard deviation in proportions | DEXSeq | stageR following DEXSeq | Citing methods in published research | DTU analysis complements DGE analysis | DGE analysis with DESeq2 | DGE analysis with edgeR | End of workflow section | Discussion | Session information | Software versions | Data availability | Acknowledgments | References