Man pages for jdwiyanto/mbiome
A convenient wrapper to visualise and run core analyses for multi-variable microbiome data
| jd_age_dec | Convert age (numeric) to categorical variable (by decades) |
| jd_alpha_stat | Calculates alpha-diversity statistics |
| jd_annotate | Extract taxa names. jd_annotate_path() is specifically for... |
| jd_bmi_cat | Convert BMI (numeric) to category |
| jd_bp_cat | Convert BP systolic and diastolic (numeric) to category |
| jd_clr | Transform raw read counts using centered-log transformation... |
| jd_dada2 | Run DADA2 ASV inference from primer- and adapter-removed... |
| jd_deseq | Calculates differential abundance statistics based on DESeq2 |
| jd_permanova | Calculates PERMANOVA |
| jd_plot_alpha | Plot alpha diversity based on selected variables |
| jd_plot_alpha2 | Plots alpha-diversity with statistics |
| jd_plot_demo | Plot demographic distribution |
| jd_plot_ord | Ordinates metagenomic data based on variable(s) |
| jd_plot_rel | Plots the relative abundance of a microbiome dataset |
| jd_rds | Merge ASV sequence tables (RDS files) from DADA2 and annotate... |
| jd_spiec | Spiec Easi network analysis |
| jd_splsda | Runs PLSDA and SPLSDA for the visualisation,... |
| jd_vst | Transform raw read counts using... |
| jd_write_relbun | Calculates the relative abundance value of taxa based on the... |
