Man pages for econtijoch/Biomass-Workflow
Microbial Density Data Generation and Analysis Tools

BatchScaleScale taxonomy summary plots (output of...
BiomassWorkflowBiomassWorkflow: A Helper Package for Microbial Biomass Data...
BR_samples_rawRaw Fluorescence data for the plate measured with Broad-Range...
BR_standard_mappingMapping file for the plate containing Broad-Range dye...
convert_to_biom_friendlyFunction to convert scaled/unscaled output of...
convert_to_lefseConvert to lefse-friendly
convert_to_phyloseqFunction to convert sequencing object to phyloseq object with...
DataAnalysisMain function call to generate microbial density data from...
Deprecated_DataAnalysisDeprecated function for Data Analysis. See DataAnalysis...
Deprecated_ParsePlateReaderFileDeprecated plate reader file parser
Deprecated_StandardAnalysisDeprecated function to process standards information and...
dropcolumnsSimple function to remove columns that are only comprised of...
EJC_colorsColor Scheme function for plotting
EJC_themeTheme function for plotting
EJC_theme_tiltedTheme function for plotting with tilted axes
ElisaAnalysisFunction to process ELISA data
Empty_weightsEmpty tube weight file
Full_weightsFull tube weight file
geom_mean_semNew layer function that plots both the summary statistics AND...
get_legendCreate a stand-alone legend for plotting
ggnameggname Helper function taken from ggplot2 - not exported,...
HS_samples_rawRaw Fluorescence data for the plate measured with...
HS_standard_mappingMapping file for the plate containing High-Sensitivity dye...
IgAAnalysisFunction to process Fecal IgA Elisa data
individual_scaleFunction to process 16S sequencing data and scale individual...
level_reorderReorder factor levels
make_biom_tablesMake biom tables (relative abundance and absolute abundance)...
mapping_fileMapping file for samples in microbial density experiment
mass_and_orderGenerate sample mass and final order of tubes. Will attempt...
matrix_plate_parserMatrix plate parser
ordinate_sequencingOrdination of scaled sequencing object
Other_DataFully processed other data (.csv)
paper_themeTheme function for plotting paper-ready figures
paper_theme_tiltedTheme function for plotting paper-ready figures with tilted...
ParseMappingFileFunction to read in mapping file and tweak format so that it...
percentquick conversion to percent
phyla_colorsColor Scheme function for phyla
pipePipe operator
PlateParserFunction to read in mapping file and tweak format so that it...
plate_to_tablePlate to table
plotterFunction to generate an interactive data plotter
predictorHelper function for IgA Elisa data generation from standard...
qubit_mergerFunction to improve accuracy of DNA measurements for samples...
read_label_pairingsRead Label Pairings
robot_prep_16SFunction to produce a Beckmann Robot-friendly file and table...
robot_prep_metagenomicsFunction to produce a Beckmann Robot-friendly file and table...
sample_file_makerFunction to generate sample data files to work wtih locally
Sample_infoSample Info for samples in microbial density experiment
scale_and_visualizeFunction to perform individual_scale function AND...
sequencing_analysis_wrapperSequencing Analysis Wrapper
sequencing_data_plotterMake abundance bar plots of sequencing data
sequencing_data_vizShiny App that aids in vizualizing sequencing objects...
sequencing_prep_16SFunction to produce files necessary to generate 16S...
sequencing_prep_metagenomicsFunction to produce files necessary to generate metagenomic...
sigmoid_modelHelper function for IgA Elisa standard curve fitting
slides_themeTheme function for plotting presentation-ready figures
slides_theme_tiltedTheme function for plotting presentation-ready figures with...
StandardAnalysisFunction to process standards information and create line of...
Standards_rawRaw Fluorescence data for the plate containing standards
stat_mean_semLayer function for stat
taxonomy_parserFunction to parse greengenes taxonomy file for use with...
Tube_orderTube Order from 96-well format barcode scanner (.csv)
well_parserFunction to toggle between a well ID and a well location...
wet_dry_weightWet vs Dry Weight calculation
econtijoch/Biomass-Workflow documentation built on May 24, 2018, 7:26 p.m.