Man pages for LucasBusta/phyloChemistry
Chemical and Sequence Analyses in a Phylogenetic Context

alignSeqsAlign sequences
alignSmilesAlign a matrix of parsed SMILES
barsCalculates mean and standard deviation
blastTranscriptsBLAST seach local transcriptomes
buildTreeCompute various types of phylogenetic trees for various types...
collapseTreeCreate a high-level cladogram from a low-level tree
convertSmilesToPubChemIDsLoads taxonomical data and a phylogenetic tree into a...
drawAlignmentGenerate a multiple alignment graphic using ggplot
extractORFsImport chemcial data
extractTaxaFromParsedSciFinderResultsImport chromatograms stored as .csv files
fadsArabidopsis QTL data on gravitropism
getNCBISeqsDownload sequences from NCBI
getPMIDsForCASIDsLoads taxonomical data and a phylogenetic tree into a...
getPMIDsForPCIDsLoads taxonomical data and a phylogenetic tree into a...
getTranscriptomesDownload transcriptomes
loadChemistryImport chemcial data
loadSeqlistParses and binds a seqlist to a phylochemistry object
loadTaxaLoads taxonomical data and a phylogenetic tree into a...
normalizeNormalizes a vector of numbers to a range of zero to one.
parseSciFinderResultsImport chromatograms stored as .csv files
parseSmilesparse SMILES notation
readChromatogramsImport chromatograms stored as .csv files
readSpectraImport mass spectral data
searchPMIDsForTaxaLoads taxonomical data and a phylogenetic tree into a...
searchTextForTaxaCount occurrences of species names in a text file
subsetSummaryImport chemcial data
ticksImport chromatograms stored as .csv files
updateCountDataImport chromatograms stored as .csv files
LucasBusta/phyloChemistry documentation built on Jan. 20, 2019, 3:55 a.m.