Man pages for econtijoch/Biomass-Workflow
Microbial Density Data Generation and Analysis Tools
| BatchScale | Scale taxonomy summary plots (output of... |
| BiomassWorkflow | BiomassWorkflow: A Helper Package for Microbial Biomass Data... |
| BR_samples_raw | Raw Fluorescence data for the plate measured with Broad-Range... |
| BR_standard_mapping | Mapping file for the plate containing Broad-Range dye... |
| convert_to_biom_friendly | Function to convert scaled/unscaled output of... |
| convert_to_lefse | Convert to lefse-friendly |
| convert_to_phyloseq | Function to convert sequencing object to phyloseq object with... |
| DataAnalysis | Main function call to generate microbial density data from... |
| Deprecated_DataAnalysis | Deprecated function for Data Analysis. See DataAnalysis... |
| Deprecated_ParsePlateReaderFile | Deprecated plate reader file parser |
| Deprecated_StandardAnalysis | Deprecated function to process standards information and... |
| dropcolumns | Simple function to remove columns that are only comprised of... |
| EJC_colors | Color Scheme function for plotting |
| EJC_theme | Theme function for plotting |
| EJC_theme_tilted | Theme function for plotting with tilted axes |
| ElisaAnalysis | Function to process ELISA data |
| Empty_weights | Empty tube weight file |
| Full_weights | Full tube weight file |
| geom_mean_sem | New layer function that plots both the summary statistics AND... |
| get_legend | Create a stand-alone legend for plotting |
| ggname | ggname Helper function taken from ggplot2 - not exported,... |
| HS_samples_raw | Raw Fluorescence data for the plate measured with... |
| HS_standard_mapping | Mapping file for the plate containing High-Sensitivity dye... |
| IgAAnalysis | Function to process Fecal IgA Elisa data |
| individual_scale | Function to process 16S sequencing data and scale individual... |
| level_reorder | Reorder factor levels |
| make_biom_tables | Make biom tables (relative abundance and absolute abundance)... |
| mapping_file | Mapping file for samples in microbial density experiment |
| mass_and_order | Generate sample mass and final order of tubes. Will attempt... |
| matrix_plate_parser | Matrix plate parser |
| ordinate_sequencing | Ordination of scaled sequencing object |
| Other_Data | Fully processed other data (.csv) |
| paper_theme | Theme function for plotting paper-ready figures |
| paper_theme_tilted | Theme function for plotting paper-ready figures with tilted... |
| ParseMappingFile | Function to read in mapping file and tweak format so that it... |
| percent | quick conversion to percent |
| phyla_colors | Color Scheme function for phyla |
| pipe | Pipe operator |
| PlateParser | Function to read in mapping file and tweak format so that it... |
| plate_to_table | Plate to table |
| plotter | Function to generate an interactive data plotter |
| predictor | Helper function for IgA Elisa data generation from standard... |
| qubit_merger | Function to improve accuracy of DNA measurements for samples... |
| read_label_pairings | Read Label Pairings |
| robot_prep_16S | Function to produce a Beckmann Robot-friendly file and table... |
| robot_prep_metagenomics | Function to produce a Beckmann Robot-friendly file and table... |
| sample_file_maker | Function to generate sample data files to work wtih locally |
| Sample_info | Sample Info for samples in microbial density experiment |
| scale_and_visualize | Function to perform individual_scale function AND... |
| sequencing_analysis_wrapper | Sequencing Analysis Wrapper |
| sequencing_data_plotter | Make abundance bar plots of sequencing data |
| sequencing_data_viz | Shiny App that aids in vizualizing sequencing objects... |
| sequencing_prep_16S | Function to produce files necessary to generate 16S... |
| sequencing_prep_metagenomics | Function to produce files necessary to generate metagenomic... |
| sigmoid_model | Helper function for IgA Elisa standard curve fitting |
| slides_theme | Theme function for plotting presentation-ready figures |
| slides_theme_tilted | Theme function for plotting presentation-ready figures with... |
| StandardAnalysis | Function to process standards information and create line of... |
| Standards_raw | Raw Fluorescence data for the plate containing standards |
| stat_mean_sem | Layer function for stat |
| taxonomy_parser | Function to parse greengenes taxonomy file for use with... |
| Tube_order | Tube Order from 96-well format barcode scanner (.csv) |
| well_parser | Function to toggle between a well ID and a well location... |
| wet_dry_weight | Wet vs Dry Weight calculation |
