Fast and Efficient (Automated) Analysis of Sparse Omics Data
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Documentation for package ‘OmicFlow’ version 1.4.0
Help Pages
| bray | Compute Bray-Curtis Dissimilarity from a Sparse Matrix. |
| canberra | Compute Canberra Dissimilarity from a Sparse Matrix. |
| colormap | Color map of a variable |
| column_exists | Checks if column exists in table |
| composition_plot | Compositional plot |
| cosine | Compute Cosine Dissimilarity from a Sparse Matrix. |
| diversity | Sparse implementation of Alpha Diversity Metrics |
| diversity_plot | Diversity plot |
| foldchange | Computes Log2(A) - Log2(B) Fold Change of (non-) paired data. |
| hill_taxa | Sparse implementation of Hill numbers |
| jaccard | Compute Jaccard Dissimilarity from a Sparse Matrix. |
| jsd | Compute Jensen-Shannon Divergence from a Sparse Matrix. |
| manhattan | Compute Manhattan Dissimilarity from a Sparse Matrix. |
| metagenomics | Sub-class metagenomics |
| omics | Abstract omics class |
| ordination_plot | Ordination plot |
| pairwise_adonis | Pairwise adonis2 (PERMANOVA) computation |
| pairwise_anosim | Pairwise anosim (ANOSIM) computation |
| plot_pairwise_stats | Create pairwise stats plot |
| proteomics | Sub-class proteomics |
| read_rarefraction_qiime | Loads a rarefied alpha diversity table from Qiime2 |
| sparse_to_dtable | Converting a sparse matrix to data.table |
| unifrac | Compute UniFrac Dissimilarity from a Sparse Matrix. |
| volcano_plot | Volcano plot |