Introduction | Installation | Loading iscream | tabix() | Setup | Making queries | Using r Biocpkg("GenomicRanges") | Setting column names | Rsamtools-style output | WGBS BED files | summarize_regions() | make_mat() | Further reading | Session info | References

One file | Multiple files | Parsing records into a data frame | Multiple files as data frame | All benchmarks | Runtime | Session info

Setup | Input BED files | Regions | Multithreading | tabix() | summarize_regions | make_mat | Session info | References

Setup | Download the data | Using tabix() | Get the Transcription start sites and flanking regions | Make a tabix query of the TSS flanking regions | Summarize average methylation profile around TSS | Plot average methylation profiles around the TSS | Using summarize_regions | Session info

r Biocpkg("GenomicRanges") | From tabix queries | From summarize_regions() | From make_mat | r Biocpkg("SummarizedExperiment") | Making BSseq objects | Session info

Conda/miniconda/mamba/micromamba | Pixi | Session info

Datasets | References

Setup | Importing Seahorse rates data | Normalization | Calculating energetics | Partitioning data | Alternative data formats | Mito + Glyco (our default) | Data in the form of @mookerjee2017 | Just Mito | Respiratory control ratio (RCR) and glycolytic capacity (GC) assay | Plotting | Bioenergetic scope plot | Replicates combined | Replicates as random effects | Replicates separated | Rate plots | Oxygen consumption rate (OCR) | Extracellular Acidification Rate (ECAR) | ATP plots | Basal glycolysis | Basal respiration | Maximal glycolysis | Maximal respiration | Customizing plots | Colors | Labels | Change axis labels | Change label size | Editing functions | References