1 curatedBladderData: Clinically Annotated Data for the Bladder Cancer Transcriptome | 2 Data access and caching | 3 Load data sets | 4 Load datasets based on rules | 5 Non-unique gene symbols | A Available Clinical Characteristics | B Summarizing the List of ExpressionSets | C For non-R users | D Session Info

Prerequisites | Update from previous stable versions | Installation | Prepare environment and assay-specific reference files | Create VCF files | Run PureCN with internal segmentation | Coverage | NormalDB | PureCN | Run PureCN with third-party segmentation | General usage | Recommended CNVkit usage | Recommended GATK4 usage | Biomarkers | Reference

1 Introduction | 2 Basic input files | 3 Library-specific coverage bias | 4 Pool of normals | 5 Recommended run | 6 Output | 7 Curation | 8 Cell lines | 9 Maximizing the number of heterozygous SNPs | 10 Advanced usage | 11 Limitations | 12 Support