Overview | Basics | Installing recount3 | Required knowledge | Asking for help | Citing r Biocpkg('recount3') | Quick start | Users guide | Available data | Terminology | Available annotations | Build a RSE | Explore the RSE | Sample metadata | Counts | Exon | Exon-exon junctions | BigWig files | Local files | Your own mirror | Teams involved | Project history | Other related tools | Reproducibility | Bibliography

r Biocpkg('bumphunter') example | Reproducibility

Basics | Install r Biocpkg('derfinder') | Required knowledge | Asking for help | Citing r Biocpkg('derfinder') | Quick start to using to r Biocpkg('derfinder') | Introduction | Sample DER Finder analysis | Reproducibility | Bibliography

Basics | Install r Biocpkg('regionReport') | Required knowledge | Asking for help | Citing r Biocpkg('regionReport') | HTML reports for a set differential region results | Using r Biocpkg('regionReport') for r Biocpkg('DESeq2') results | Example | Using r Biocpkg('regionReport') for r Biocpkg('edgeR') results | Using r Biocpkg('regionReport') for region results | Examples | General case | r Biocpkg('derfinder') single base-level case | Run r Biocpkg('derfinder') | Create report | Notes | Reproducibility | Bibliography

Welcome | Study design | Shiny website mirrors | Basics | Install spatialLIBD | Required knowledge | Asking for help | Citing spatialLIBD | Overview | Human DLPFC Visium dataset | Data specifics | Downloading the data with spatialLIBD | Interactively explore the spatialLIBD data | spatialLIBD functions | Spot-level clusters and discrete variables | Spot-level genes and continuous variables | Extract significant genes | Visualize modeling results | Correlation of layer-level statistics | Gene set enrichment | Re-shaping your data to our structure | SpatialExperiment support | Using spatialLIBD with your own data | Expected characteristics of the data | Generating our data (legacy) | More spatially-resolved LIBD datasets | spatialDLPFC | Visium_SPG_AD | LIBD data outside spatialLIBD | locus-c | Reproducibility | Bibliography

Plotting One Gene | Plotting Multiple Genes | Averaging Z-scores | Summarizing with PCA | Plotting Sparsity of Expression | With more marker genes | Visualizing non-gene continuous variables | Reproducibility | Bibliography

Basics | Install r Biocpkg('recount') | Required knowledge | Asking for help | Workflow using r Biocpkg('recount') | Citing r Biocpkg('recount') | Quick start to using to r Biocpkg('recount') | Introduction | Sample DE analysis | Download data | Finding phenotype information | Predicted phenotype information | DE analysis | Report results | Finding gene names | Sample r Biocpkg('derfinder') analysis | Define expressed regions | Compute coverage matrix | Construct a DESeqDataSet object | r Biocpkg('DESeq2') analysis | Annotation used | Using another/newer annotation | Candidate gene fusions | Snaptron | FANTOM-CAT annotation | recount-brain | Download all the data | Accessing r Biocpkg('recount') via SciServer | Step by step | SciServer help | Citing SciServer | Reproducibility | Bibliography

Overview | Data | Reproducibility | Bibliography

Basics | Install r Biocpkg('derfinderHelper') | Required knowledge | Asking for help | Citing r Biocpkg('derfinderHelper') | Introduction to r Biocpkg('derfinderHelper') | Example | Data | Models | Get F-statistics | Details | Reproducibility | Bibliography

Asking for help | r Biocpkg('derfinder') users guide | Expressed regions-level | regionMatrix() | railMatrix() | Single base-level F-statistics | Example data | Phenotype data | Load the data | Filter coverage | Expressed region-level analysis | Via regionMatrix() | Find DERs with r Biocpkg('DESeq2') | Find DERs with r Biocpkg('limma') | Via railMatrix() | Single base-level F-statistics analysis | Models | Find candidate DERs | Explore results | optionStats | coveragePrep | fstats | regions | Nearest annotation | Time spent | Merge results | optionsMerge | fullRegions | fullAnnotatedRegions | ChIP-seq differential binding | Visually explore results | Interactive HTML reports | Miscellaneous features | Feature level analysis | Compare results visually | Export coverage to BigWig files | Advanced arguments | Non-human data | Functions that use multiple cores | Loading data details | Controlling loading from BAM files | Unfiltered base-level coverage | Input files in a different naming style | Loading data in chunks | Large number of samples | Flow charts | DER analysis flow chart | analyzeChr() flow chart | regionMatrix() flow chart | Base-level F-statistics projects | File organization | bash scripts | derfinder-analysis.R | derAnalysis.sh | Expressed regions-level projects | Summary | Reproducibility | Bibliography

What is Spatial Registration? | Overview of the Spatial Registration method | How to run Spatial Registration with spatialLIBD tools | Introduction. | Important Notes | Required knowledge | Citing spatialLIBD | Setup | Install spatialLIBD | Load required packages | Download Data | Spatial Reference | Query Data: snRNA-seq | Get Enrichment statistics for snRNA-seq data | Extract Enrichment t-statistics | Correlate statsics with Layer Reference | Explore Results | Create Heatmap of Correlations | Annotate Cell Types by Top Correlation | Plot Annotated Cell Types | Reproducibility | Bibliography

Basics | Backstory | Styling code | GitHub Actions | Motivation | Developing a Bioconductor-friendly GHA workflow | Potential future additions | Wrapping up | usethis-like functions | Acknowledgments | Reproducibility | Bibliography

Basics | Install biocthis | Required knowledge | Asking for help | Citing biocthis | Quick start to using to biocthis | Using biocthis in your R package | biocthis functions overview | use_bioc_badges() | bioc_style() | use_bioc_citation() | use_bioc_description() | use_bioc_feature_request_template() | use_bioc_github_action() | Getting started | Main GHA workflow features | Additional features | Configure options | Automatically scheduled tests | Notes about GHA workflows | use_bioc_issue_template() | use_bioc_news_md() | use_bioc_pkg_templates() | use_bioc_pkgdown_css() | use_bioc_readme_rmd() | use_bioc_support() | use_bioc_vignette() | Acknowledgments | Reproducibility | Bibliography

Basics | Install spatialLIBD | Required knowledge | Citing spatialLIBD | Download data from 10x Genomics | Load packages | Download spaceranger output files | Modify spe for spatialLIBD | Add gene annotation information | From 10x | From Gencode | Enable a friendlier gene search | Filter the spe object | Check object | Explore the data | Run the interactive website | Wrapper functions | Publishing your web application | Limitations | Memory | Response speeds | Image resolution | Customization | Reproducibility | Bibliography