| AA | A character vector of amino acids. |
| Abbrev | A data frame with metabolite naming conventions used in this... |
| Adenine | A character vector of adenine-related compounds. |
| bar | This function produces a bar plot using data from function... |
| bar_plot | This function produces a bar plot using data from function... |
| CoAs | A character vector of co-enzyme A-related compounds. |
| colors | A character vector of commonly used colors. |
| CompMZ | A data frame with compound information for 15710 from the... |
| compound.pathway | A data frame of 3443 KEGG metabolites and their association... |
| compounds | A data frame of 18042 KEGG compounds. |
| Curr | A character vector of currency metabolites. |
| Cys | A character vector of cysteine metabolism compounds. |
| Cytosine | A character vector of cytosine-related compounds. |
| data_annotate | This function is searching either the KEGG or HMDB databases... |
| FA | A character vector of fatty acid-related compounds. |
| Fru | A character vector of fructose metabolism compounds. |
| gene.pathway | A data frame of genes associated with 319 KEGG pathways. This... |
| glycolysis | A character vector of glycolysis compounds. |
| Guanine | A character vector of guanine metabolism compounds. |
| Hex | A character vector of hexose metabolism compounds. |
| isobar | This function takes in an m/z value and will return all... |
| isomer | This function takes in a chemical formula and will return all... |
| isomer_KEGG | This function takes in a chemical formula and will return all... |
| KEGG.pathway | A data frame with 514 KEGG pathways and their corresponding... |
| make_AOV_volcano | This function takes in a data and produces a volcano plot... |
| make_FC | This function produces a data frame with fractional... |
| make_INCA | Create a tab-delimited file with MDVs and a csv file with FC... |
| make_INCA_normalized | Creates a csv file with flux estimates relative to a control... |
| make_labeled | This function produces a data frame with percent labeled... |
| make_line_graph | This function produces a data frame with mass isotopologue... |
| make_matrix | This function produces a matrix for hierarchical clustering... |
| make_MID | This function produces a data frame with mass isotopologue... |
| make_mzXML | This function converts .raw files into .mzXML files for... |
| make_PCA | This function takes in a data matrix and produces a PCA plot... |
| make_PCA2 | This function takes in a data matrix and produces a PCA plot... |
| make_pheatmap | This function takes in a data matrix and produces an... |
| make_RelAmounts | This function produces a data frame with relative metabolite... |
| make_unlabeled | This function produces a data frame with fractional... |
| make_volcano | This function produces a volcano plot using data with two... |
| mapvalues | This function uses the mapvalues function from plyr without... |
| Neurotrans | A character vector of neurotransmitter compounds. |
| normal | A character vector of colors used in heatmaps. |
| paths | A list with all information for 319 KEGG pathways. |
| PPP | A character vector of pentose phosphate metabolism compounds. |
| purine | A character vector of purine metabolism compounds. |
| pyrimidine | A character vector of pyrimidine metabolism compounds. |
| QE | A character vector of compounds to be used as MID inputs for... |
| TCA | A character vector of Tricarboxylic acid (TCA) metabolism... |
| Thymine | A character vector of thymine metabolism compounds. |
| Uracil | A character vector of uracil metabolism compounds. |
