Man pages for robertdouglasmorrison/DuffyTools
Duffy Lab Utility Tools

AAtoCodonOptimizedDNAConvert Amino Acid sequence to Codon Optimized DNA
addMapSetAdd Organism Annotation MapSet to DuffyTools environment
addTargetAdd a Target Organism(s) to DuffyTools Environment
alias2GeneConvert gene aliases to standardized gene identifiers.
allowCompressedFileNameAllow .gz filename extensions
annotationTableExtract facts from an Annotation Table
as.FastaConvert to FASTA list format
as.percentFormat Numbers as Percentages
as.rankPercentileConvert to Rank Percentiles
as.TRUEorFALSEResolve 'anything' to a logical value
averageLineWithErrorBarsAdd error bars to an existing plot
baseDepthTableBase Depth Tables and Vectors
blastToolsCall BLAST and/or read results from a BLAST query
BScountToPctParasitemiaConversion Functions for Parasite Infection Measurements.
calcRPlow level Rank Product function
calcTMMelting Temperature (Tm) of an oligo probe
cgFractionPercentage of C and G bases in a DNA sequence
checkDuffyPackagesCheck for Packages used by DuffyTools
clipFastqFileClip Bases from FASTQ reads
colorBySpeciesAssign colors by SpeciesID
consensusRankConsensus Ranking of Genes
convertGenomicBasesToCodingAAConversions Between DNA and AA in Chromosome or Gene Local...
convertHypertextConvert Hypertext special characters
DESeq.DiffExpressDifferential Expression by Group functions
diffExpressRankOrderOrder Differentially Expressed Genes
DKMshiftDensity Kernel Mode Linear Shift
DNAtoAADNA Codon to Amino Acid Peptide Conversion routines
duffyRMARobust Multichip Average (RMA)
DuffyToolsDuffy Lab "Tools" package Overview
elapsedProcTimeProvide processing timing information
enrichmentEnrichment Compared To Chance
env.subEnvironment Variable Substitution
exportCurrentMapSetExport the Current Annotation MapSet
exportTargetsExport or Import all Targets
expressionClusterClustering of Gene Expression Data
expressionFileSetToMatrixConvert Expression Files to/from a Matrix of Gene Values
expressionHeatmapHeatmap of Gene Expression Matrix
expressionMatrixToDElistTurn a Matrix of Gene Expression into a List of Differential...
expressionMatrixToMvalueTurn a matrix of Gene Expression into M-values
fastqPatternSearchFind DNA Patterns in FASTQ Reads
fastqToFastaConvert FASTQ to FASTA
fastSeqID2SpeciesSeqID to SpeciesID Lookup
fastSeqPos2GenePosSequence Positon to GeneID and Details
file.cleanSpecialCharactersFromFileNameClean Special Character from Filenames
gatherGeneSetsGather Named Sets of Genes
gaussianGenerate and/or Fit Gaussian Data
gene2AliasConvert from a GeneID to a set of known aliases.
gene2ProductGene Product Description
geneSetAnalysisPathway and Gene Set Analysis using Density Curves
geneSetEnrichmentGene Pathway Enrichment
getCodonMapGet DNA Codon & Amino Acid Map
getCurrentGeneMapGet the Current GeneMap
getCurrentSpeciesGet Current Species
getCurrentTargetGet Current Target
getDensityKernelModeMode of the Density Kernel
getFastaSeqFromFilePathGenomic DNA sequence for one SeqID
getFileLineCountManange Line and Read Counts for Large Files
getGlobalMetricsGlobal Metrics of Expression Data
getHumanIDtermsCommon Human GeneID Terms
getSamplePairIDsSampleIDs for Paired End Datasets
getSpeciesFromSeqIDSpecies Identifier Converters
getVargeneDomainMapVariable Surface Antigen Maps
globalNormalizeNormalize Microarray Intensity
importMapSetImport Annotation MapSet Files
levenshteinLevenshtein String Edit Distance
loadFastaRead or write a FASTA File
localityPlotPlot Gene Locations on Chromosomes
logmeanLog-Average or Geometric Mean
MapSetsDuffy Lab "MapSets" Overview
mergeTablesMerge 1-D Tables
metaRanksMeta Ranking of Transcriptome Genes
metaResultsMetaRank Summary of Differential Expression Results
movingAverageMoving Average
multicore.samplePairsMulticore Processing Wrappers
multicore.setupMulticore Processing Wrappers
myReverseComplementReverse Complement of DNA nucleotides
normalFunctions for generating and fitting named distribution...
oneDtableTable from a 1-D vector
openCompressedFileOpen a Compressed File
optionsTableExtract Facts from an Options Table
orthologGene Orthologs
phredScoreStringToIntConvert Phred Quality Score Strings to Integers
pipe.GeneSetAnalysisPathway and Gene Module Analysis
pipe.GeneSetEnrichmentGene Module and Pathway Enrichment
plotMetaResultsDeviation Plots for Meta Results
plotTranscriptsScatterplot or MA plot
rankEquivIntensityQuantile Normalize
rankProductDiffExpressRank Product across multiple Samples
readALNfileRead and Write Clustal .ALN and .NXS files
readFastqFileRead and write FASTQ Files
SAM.DiffExpressUse SAM for Differential Expression
SAM.diffExpressRankOrderOrder Differentially Expressed Genes
setCurrentSpeciesChange the Current Species
setCurrentTargetChange the Current Target
shortGeneNameShorten GeneIDs for Simplicity
significantGenesSelect Significant Genes from a Differential Expression...
spawnRcmdLaunch R Command as a Child Process
SpeciesSpecies Overview
sqrtmeanGeneralized Mean for P=0.5
table2htmlConvert Data Frame to HTML file
TargetsTarget Organisms
tempFolderCreate a Temporary Folder on an available file system tree
tukey.meanAveraging via Tukey's Biweight
validateMapSetMapSet Self-Consistency Validation
vsaTo3D7Variable Surface Antigen Genes
robertdouglasmorrison/DuffyTools documentation built on Jan. 11, 2019, 5:38 p.m.