Man pages for Jtrachsel/funfuns
Functions I Use (Title Case)
| adapt_tsne | wrapper for rtsne function that will set perplexity to 1 if... |
| ccrepe_to_geomnet | filter ccrepe object and prepare for geomnet plotting |
| cum_dist_to_targets | Cumulative distance to targets in a distance matrix |
| darken | Return a darker hue of a color |
| DESeq_cov_asso | DESeq2 covariate associations with OTUs |
| DESeq_difabund | DESeq2 differential abundance for all treatments compared to... |
| Deseq.quickplot | Quickly plot Deseq2 results |
| extract_mothur_tax | Extract mothur SILVA formatted taxonomy |
| gather_nodes | Collect type information for nodes in a network |
| iterative_dist_remove | iteratively remove objects from a distance matrix and plot at... |
| iter_plots | plots the output of iterative_NMDS |
| lighten | Return a lighter hue of a color |
| min_dist_to_targets | Minimum distance to targets for each other entry in a... |
| NMDS_ellipse | Generate NMDS points, group centroids and standard error... |
| otu_tax_labels | swap OTU designations with 'genus:OTU' |
| pairwise.adonis | this function taken from... |
| prune_graph | Remove small unconnected subnetworks from a network |
| qpcr_DDCT | CTs to log2 fold change relative to controls |
| qpcr_DDCT_LOD | CTs to log2 fold change relative to controls with LOD... |
| rcorr_to_geomnet | filter rcorr object and prepare for geomnet plotting |
| read_mash_tri | Read in a mash output lower triangle file as a dist object |
| topGO_wrapper | Wrapper for TopGO - GO term enrichment analysis |
