Man pages for kkrismer/transite
RNA-binding protein motif analysis

calculateKmerEnrichment_k_-mer Enrichment between Foreground and Background Sets
calculateKmerScores_k_-mer Score Calculation
calculateLocalConsistencyLocal Consistency Score
calculateMotifEnrichmentBinding Site Enrichment Value Calculation
calculateTranscriptMCMotif Enrichment calculation
checkKmersCheck Validity of Set of _k_-mers
computeKmerEnrichment_k_-mer Enrichment between Foreground and Background Sets
computeMotifScoreMotif Score Algorithm
createKmerMotifCreates Transite motif object from character vector of...
createMatrixMotifCreates Transite motif object from position weight matrix
drawVolcanoPlot_k_-mer Enrichment Volcano Plot
empiricalEnrichmentMeanCDFSignificance of Observed Mean
geToy Gene Expression Data Set
generateIUPACByKmersGenerates IUPAC code for a character vector of _k_-mers
generateIUPACByMatrixGenerates IUPAC code for motif matrix
generateKmers_k_-mer Counts for Sequence Set
generateKmersFromIUPACGenerates all _k_-mers for IUPAC string
generatePermutedEnrichmentsGenerate Random Permutations of the Enrichment Data
geometricMeanGeometric Mean
getMotifByIdRetrieve motif objects by id
getMotifByRBPRetrieve motif objects by gene symbol
getMotifsRetrieve list of all motifs
getPPMGet Position Probability Matrix (PPM) from motif object
homopolymerCorrectionCorrection for Homopolymeric Stretches
initIUPAClookupTableInitializes the IUPAC lookup table
kmers.enrichmentExample _k_-mer Enrichment Data
lookupKmerScores_k_-mer Score Lookup Table Access Function
motifsTransite Motif Database
motifsMetaInfoDisplays motif meta information.
pCombineP-value aggregation
permTestGeometricMeanPermutation Test Based Significance of Observed Mean
RBPMotif-classAn S4 class to represent a RBPMotif
runKmerSPMA_k_-mer-based Spectrum Motif Analysis
runKmerTSMA_k_-mer-based Transcript Set Motif Analysis
runMatrixSPMAMatrix-based Spectrum Motif Analysis
runMatrixTSMAMatrix-based Transcript Set Motif Analysis
scoreSequencesScore Sequences with PWM
scoreSpectrumCalculates spectrum scores and creates spectrum plots
scoreTranscriptsScores transcripts with position weight matrices
scoreTranscriptsSingleMotifScores transadsadscripts with position weight matrices
setMotifsSet Transite motif database
spectrumClassifierSimple spectrum classifier based on empirical thresholds
SpectrumScore-classAn S4 class to represent a scored spectrum
subdivideDataSubdivides Sequences into _n_ Bins
toy.motif.matrixToy Motif Matrix
kkrismer/transite documentation built on Nov. 6, 2019, 12:10 p.m.