reconsi package: vignette | Introduction | Installation | General use | Case study | Session info

Introduction | Publication | Installation | Analysis | Dataset | Unconstrained RCM | Fitting the unconstrained RCM | Adding dimensions | Conditioning | Plotting the uconstrained RCM | Monoplots | Biplots | Adding projections | Assessing the goodness of fit | Testing significance of clusters using PERMANOVA | Constrained RCM | Fitting the constrained RCM model | Plotting the constrained RCM model | Sample-taxon biplot | Variable-taxon biplot | Triplot | Identifying influential observations | Importance of dimensions | Importance parameters \psi | Log-likelihoods | Inertia | Advanced plotting | Extracting coodinates | Non-squared plots | FAQ | Why are not all my samples shown in the constrained ordination? | Session info

combi package: vignette | Introduction | Installation | Unconstrained integration | Adding projections | Coordinates | Constrained integration | Diagnostics | FAQ | Why are not all my samples shown in the constrained ordination? | The combi function crashes, what should I do | Session info

Contents | Introduction to SPsimSeq | Installing SPsimSeq | Demonstration | Example 1: simulating bulk RNA-seq | Example 2: simulating single-cell RNA-seq (containing read-counts) | References

Obtaining the original data | Processing the drug similarities | Obtaining the data | Calculating the similarities

Concepts and terms used in the package. | Notation and naming of networks in the package | Data in the package | Homogeneous networks | Heterogeneous networks | Fitting a two-step kernel ridge regression | Heterogeneous network | Homogeneous network | Extracting parameters from a trained model. | Information on the fit of the model | Performing leave-one-out cross-validation | Settings for LOO | Use LOO in other functions | Looking at model output | Tuning a model to find the best lambda. | Predicting new values | Predict for new K-nodes | Predict for new G-nodes | Predict for new K and G nodes | Impute new values based on a tskrr model

Virtual classes | Actual classes | Inheritance from tskrr | Slots defined by tskrrHomogeneous | Slots defined by tskrrHeterogeneous | Inheritance from tskrrTune | Inheritance from tskrrImpute