Man pages for robertdouglasmorrison/DuffyTools
Duffy Lab Utility Tools
| AAtoCodonOptimizedDNA | Convert Amino Acid sequence to Codon Optimized DNA |
| addMapSet | Add Organism Annotation MapSet to DuffyTools environment |
| addTarget | Add a Target Organism(s) to DuffyTools Environment |
| alias2Gene | Convert gene aliases to standardized gene identifiers. |
| allowCompressedFileName | Allow .gz filename extensions |
| annotationTable | Extract facts from an Annotation Table |
| as.Fasta | Convert to FASTA list format |
| as.percent | Format Numbers as Percentages |
| as.rankPercentile | Convert to Rank Percentiles |
| as.TRUEorFALSE | Resolve 'anything' to a logical value |
| averageLineWithErrorBars | Add error bars to an existing plot |
| baseDepthTable | Base Depth Tables and Vectors |
| blastTools | Call BLAST and/or read results from a BLAST query |
| BScountToPctParasitemia | Conversion Functions for Parasite Infection Measurements. |
| calcRP | low level Rank Product function |
| calcTM | Melting Temperature (Tm) of an oligo probe |
| cgFraction | Percentage of C and G bases in a DNA sequence |
| checkDuffyPackages | Check for Packages used by DuffyTools |
| clipFastqFile | Clip Bases from FASTQ reads |
| colorBySpecies | Assign colors by SpeciesID |
| consensusRank | Consensus Ranking of Genes |
| convertGenomicBasesToCodingAA | Conversions Between DNA and AA in Chromosome or Gene Local... |
| convertHypertext | Convert Hypertext special characters |
| DESeq.DiffExpress | Differential Expression by Group functions |
| diffExpressRankOrder | Order Differentially Expressed Genes |
| DKMshift | Density Kernel Mode Linear Shift |
| DNAtoAA | DNA Codon to Amino Acid Peptide Conversion routines |
| duffyRMA | Robust Multichip Average (RMA) |
| DuffyTools | Duffy Lab "Tools" package Overview |
| elapsedProcTime | Provide processing timing information |
| enrichment | Enrichment Compared To Chance |
| env.sub | Environment Variable Substitution |
| exportCurrentMapSet | Export the Current Annotation MapSet |
| exportTargets | Export or Import all Targets |
| expressionCluster | Clustering of Gene Expression Data |
| expressionFileSetToMatrix | Convert Expression Files to/from a Matrix of Gene Values |
| expressionHeatmap | Heatmap of Gene Expression Matrix |
| expressionMatrixToDElist | Turn a Matrix of Gene Expression into a List of Differential... |
| expressionMatrixToMvalue | Turn a matrix of Gene Expression into M-values |
| fastqPatternSearch | Find DNA Patterns in FASTQ Reads |
| fastqToFasta | Convert FASTQ to FASTA |
| fastSeqID2Species | SeqID to SpeciesID Lookup |
| fastSeqPos2GenePos | Sequence Positon to GeneID and Details |
| file.cleanSpecialCharactersFromFileName | Clean Special Character from Filenames |
| gatherGeneSets | Gather Named Sets of Genes |
| gaussian | Generate and/or Fit Gaussian Data |
| gene2Alias | Convert from a GeneID to a set of known aliases. |
| gene2Product | Gene Product Description |
| geneSetAnalysis | Pathway and Gene Set Analysis using Density Curves |
| geneSetEnrichment | Gene Pathway Enrichment |
| getCodonMap | Get DNA Codon & Amino Acid Map |
| getCurrentGeneMap | Get the Current GeneMap |
| getCurrentSpecies | Get Current Species |
| getCurrentTarget | Get Current Target |
| getDensityKernelMode | Mode of the Density Kernel |
| getFastaSeqFromFilePath | Genomic DNA sequence for one SeqID |
| getFileLineCount | Manange Line and Read Counts for Large Files |
| getGlobalMetrics | Global Metrics of Expression Data |
| getHumanIDterms | Common Human GeneID Terms |
| getSamplePairIDs | SampleIDs for Paired End Datasets |
| getSpeciesFromSeqID | Species Identifier Converters |
| getVargeneDomainMap | Variable Surface Antigen Maps |
| globalNormalize | Normalize Microarray Intensity |
| importMapSet | Import Annotation MapSet Files |
| levenshtein | Levenshtein String Edit Distance |
| loadFasta | Read or write a FASTA File |
| localityPlot | Plot Gene Locations on Chromosomes |
| logmean | Log-Average or Geometric Mean |
| MapSets | Duffy Lab "MapSets" Overview |
| mergeTables | Merge 1-D Tables |
| metaRanks | Meta Ranking of Transcriptome Genes |
| metaResults | MetaRank Summary of Differential Expression Results |
| movingAverage | Moving Average |
| multicore.samplePairs | Multicore Processing Wrappers |
| multicore.setup | Multicore Processing Wrappers |
| myReverseComplement | Reverse Complement of DNA nucleotides |
| normal | Functions for generating and fitting named distribution... |
| oneDtable | Table from a 1-D vector |
| openCompressedFile | Open a Compressed File |
| optionsTable | Extract Facts from an Options Table |
| ortholog | Gene Orthologs |
| phredScoreStringToInt | Convert Phred Quality Score Strings to Integers |
| pipe.GeneSetAnalysis | Pathway and Gene Module Analysis |
| pipe.GeneSetEnrichment | Gene Module and Pathway Enrichment |
| plotMetaResults | Deviation Plots for Meta Results |
| plotTranscripts | Scatterplot or MA plot |
| rankEquivIntensity | Quantile Normalize |
| rankProductDiffExpress | Rank Product across multiple Samples |
| readALNfile | Read and Write Clustal .ALN and .NXS files |
| readFastqFile | Read and write FASTQ Files |
| SAM.DiffExpress | Use SAM for Differential Expression |
| SAM.diffExpressRankOrder | Order Differentially Expressed Genes |
| setCurrentSpecies | Change the Current Species |
| setCurrentTarget | Change the Current Target |
| shortGeneName | Shorten GeneIDs for Simplicity |
| significantGenes | Select Significant Genes from a Differential Expression... |
| spawnRcmd | Launch R Command as a Child Process |
| Species | Species Overview |
| sqrtmean | Generalized Mean for P=0.5 |
| table2html | Convert Data Frame to HTML file |
| Targets | Target Organisms |
| tempFolder | Create a Temporary Folder on an available file system tree |
| tukey.mean | Averaging via Tukey's Biweight |
| validateMapSet | MapSet Self-Consistency Validation |
| vsaTo3D7 | Variable Surface Antigen Genes |
