Introduction | Installation | Input data format | Tutorial | Boundary density | Session information

Introduction | Examples | Sequencing-based spatial transcriptomics data | Spot shape - Slide-seq and Visium | Quality control (QC) plots | Spot/bin/cell-level QC | Feature-level QC | Bin shape - Visium HD | Imaging-based spatial transcriptomics data | Reduced dimension plots | Session information

Introduction | Installation | Datasets | Load data | Load using named accessors | Visium_humanDLPFC | Visium_mouseCoronal | seqFISH_mouseEmbryo | ST_mouseOB | SlideSeqV2_mouseHPC | Janesick_breastCancer_Chromium | Janesick_breastCancer_Visium | Janesick_breastCancer_Xenium_rep1 | Janesick_breastCancer_Xenium_rep2 | CosMx_lungCancer | MERSCOPE_ovarianCancer | STARmapPLUS_mouseBrain | Load by querying ExperimentHub database | Generating objects from raw data files | Session information

Introduction | Installation | Input data format | Tutorial | Standard analysis | Run nnSVG | Investigate results | With covariates | Multiple samples | Troubleshooting | Zeros (genes or spots) | Small numbers of spots | Session information

Introduction | Installation | Contents | Loading the data | Show data | Session information

Dimension reduction | Clustering | Differential analysis | Differential abundance (DA) | Differential states (DS)

Overview | Datasets | Programmatic access to list of datasets | How to load data | Using the data | Transformation of raw data | Exploring the data | Contribution guidelines | Citation

Introduction | Example workflow | Data set | Exon microarray data | Workflow | Load data and create condition vector | Run workflow with wrapper function | Summary table of results | Run workflow using functions for individual steps | Create RegspliceData object | Filter zero-count exon bins | Filter low-count exons | Calculate normalization factors | 'voom' transformation and weights | Initialize RegspliceResults object | Fit models | Calculate likelihood ratio tests | Analyze results | Summary of all significant genes | Contingency table | Additional information | Additional user options | Design matrices

Open GitHub issue | Prepare object files | Create pull request | Contact Bioconductor maintainers to upload .rda files | Acknowledgment of contributions | Code of conduct

Introduction | Overview of 'diffcyt' methodology | Summary | Differential abundance (DA) and differential states (DS) | Flexible experimental designs and contrasts | More details | Installation | 'diffcyt' pipeline | Dataset | Load data from 'HDCytoData' package | Alternatively: load data from '.fcs' files | Set up meta-data | Set up design matrix (or model formula) | Set up contrast matrix | Differential testing | Option 1: Wrapper function using input data from '.fcs' files | Option 2: Wrapper function using CATALYST 'daFrame' object | Option 3: Individual functions | Prepare data into required format | Transform data | Generate clusters | Calculate features | Test for differential abundance (DA) of cell populations | Test for differential states (DS) within cell populations | Exporting data | Visualizations using 'CATALYST' package | Overview | Heatmap: DA test results | Heatmap: DS test results | References