Overview | User-facing interface and global options | Global options | Creating, opening, and inspecting HDF5 datasets | Importing tabular data | Subsetting, assignment, dimnames, and conversion to memory | Matrix algebra | Element-wise arithmetic | Matrix multiplication | Crossproducts | Binding matrices | Statistical operations | Matrix decompositions | Singular value decomposition | Principal component analysis | QR decomposition | Cholesky decomposition and inverse | Eigen decomposition and pseudoinverse | Dataset operations: split, reduce, and apply | Split | Reduce | Apply function | Compression and HDF5 file space management | Compression | HDF5 file space management | Managing HDF5 resources | Extending BigDataStatMeth through C++ | Session information

Introduction | Data loading | Descriptive analysis | Hardy-Weinberg equilibrium | SNP association analysis | Gene-environment and gene-gene interactions | Haplotype analysis | Haplotype estimation | Haplotype association | Sliding window approach | Session info | References

Getting started | Normalization and filtering | The Poisson-Tweedie family of distributions to model RNA-seq count data | Goodness of fit to a count data distribution | Testing for differential expression | Visualizing the results | Assessing differential expression calling accuracy | Fitting generalized linear models (GLM) | Session info

Description of implemented clocks | Chronological DNAm age (in years) | Gestational DNAm age (in weeks) | Getting started | DNA Methylation clocks | Data format | Data nomalization | Missing individual's data | Missing CpGs of DNAm clocks | Cell counts | Chronological and biological DNAm age estimation | Data in Horvath's format (e.g. csv with CpGs in rows) | Age acceleration | Chronological age prediction using ExpressionSet data | Use of DNAmAge in association studies | Use of DNAm age in children | Gestational DNAm age estimation | Model predicion | Correlation among DNAm clocks | References

Introduction | Inversion characterization | Quality control | Imputed data | Other features | Inversions included in scoreInvHap | sessionInfo