Man pages for Bioconductor-mirror/SELEX
Functions for analyzing SELEX-seq data

selex.affinitiesConstruct a K-mer affinity table
selex.configSet SELEX system parameters
selex.countsConstruct or retrieve a K-mer count table
selex.countSummarySummarize available K-mer count tables
selex.defineSampleDefine annotation for an individual sample
selex.exampledataExtract example data files
selex.fastqPSFMConstruct a diagnostic PSFM for a FASTQ file
selex.getAttributesDisplay sample handle properties
selex.getRound0Obtain round zero sample handle
selex.getSeqfilterDisplay sequence filter attributes
selex.infogainCompute or retrieve information gain between rounds
selex.infogainSummarySummarize available information gain values
selex.jvmStatusDisplay current JVM memory usage
selex.kmaxCalculate kmax for a dataset
selex.kmerPSFMConstruct a PSFM from a K-mer table
selex.loadAnnotationLoad a sample annotation file
selex.mmBuild or retrieve a Markov model
selex.mmProbCompute prior probability of sequence using Markov model
selex.mmSummarySummarize Markov model properties
selex.revcompCreate forward-reverse complement data pairs
selex.runRun a standard SELEX analysis
selex.sampleCreate a sample handle
selex.samplePSFMConstruct a diagnostic PSFM for a FASTQ file
selex.sampleSummaryShow samples visible to the current SELEX session
selex.saveAnnotationSave sample annotations to file
selex.seqfilterCreate a sequence filter
selex.setwdSet or change the working directory
selex.splitRandomly split a dataset
selex.summaryDisplay all count table, Markov model, and information gain...
Bioconductor-mirror/SELEX documentation built on June 1, 2017, 1:14 a.m.