Fast and Efficient (Automated) Analysis of Sparse Omics Data
Sparse implementation of Hill numbers
Create pairwise stats plot
Compute Bray-Curtis Dissimilarity from a Dense or Sparse Matrix.
Compute Canberra Dissimilarity from a from a Dense or Sparse Matrix.
Color map of a variable
Checks if column exists in table
Compositional plot
Compute Cosine Dissimilarity from a Dense or Sparse Matrix.
Diversity plot
Sparse implementation of Alpha Diversity Metrics
Computes Log2(A) - Log2(B) Fold Change of (non-) paired data.
Compute Jaccard Dissimilarity from a Dense or Sparse Matrix.
Compute Jensen-Shannon Divergence from a Dense or Sparse Matrix.
Compute Manhattan Dissimilarity from a Dense or Sparse Matrix.
Converting a Matrix to data.table
Sub-class metagenomics
OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data
Abstract omics class
Ordination plot
Pairwise adonis2 (PERMANOVA) computation
Pairwise anosim (ANOSIM) computation
Sub-class proteomics
Compute UniFrac Dissimilarity from a Dense or Sparse Matrix.
Volcano plot
A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user, which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.