Man pages for LucasBusta/phyloChemistry
Chemical and Sequence Analyses in a Phylogenetic Context
| alignSequences | Align sequences in a seqlist |
| blastTranscriptomes | BLAST search local transcriptomes |
| buildPolylist | Build a human-readable matrix of samples, analytes, and... |
| buildTree | Construct various types of phylogenetic trees from alignments... |
| convertCDFstoCSVs | Convert mass spectral datafiles (CDF) into a csv file |
| drawAlignment | Generate a multiple alignment graphic using ggplot |
| extractChromatogramsFromCSVs | Extract total ion chromatograms from csv files containing... |
| extractORFs | Extract open reading frames from multifasta files |
| generateTicks | Create major and minor axes ticks and labels |
| integrationApp | A Shiny app to integrate GC-FID and GC-MS data |
| normalize | Normalizes a vector of numbers to a range of zero to one. |
| OsDirectoryPathCorrect | OS-aware correction of directory paths |
| phylogeneticSignal | Convert mass spectral datafiles (CDF) into a csv file |
| pruneTree | Prune a tree so it only contains user-specified tips |
| readChromatograms | Import chromatograms stored as ChemStation exported .csv... |
| readFasta | Returns contents of one fasta file as a StringSet object. |
| readGFFs | readGFFs |
| readManyFasta | Returns the contents of many fasta files as a StringSet... |
| readMonolist | Reads a monolist |
| readPolylist | Reads a polylist |
| readSpectra | Import mass spectral data |
| readTree | Reads a phylogenetic tree |
| writeFasta | Writes one or more sequences as a single fasta file |
| writeMonolist | Writes a monolist |
| writePolylist | Writes a polylist |
| writeSingleFastas | Writes one or more sequences as individual fasta file(s),... |
| writeSupplementalTable | Writes a human-readable supplemental table of quantitative... |
| writeTree | Writes a phylogenetic tree |
