Functions for analyzing SELEX-seq data

Documentation for package ‘SELEX’ version 1.19.5

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SELEX-package	SELEX Package
Selex	SELEX Package
selex	SELEX Package
selex.affinities	Construct a K-mer affinity table
selex.config	Set SELEX system parameters
selex.counts	Construct or retrieve a K-mer count table
selex.countSummary	Summarize available K-mer count tables
selex.defineSample	Define annotation for an individual sample
selex.exampledata	Extract example data files
selex.fastqPSFM	Construct a diagnostic PSFM for a FASTQ file
selex.getAttributes	Display sample handle properties
selex.getRound0	Obtain round zero sample handle
selex.getSeqfilter	Display sequence filter attributes
selex.infogain	Compute or retrieve information gain between rounds
selex.infogainSummary	Summarize available information gain values
selex.jvmStatus	Display current JVM memory usage
selex.kmax	Calculate kmax for a dataset
selex.kmerPSFM	Construct a PSFM from a K-mer table
selex.loadAnnotation	Load a sample annotation file
selex.mm	Build or retrieve a Markov model
selex.mmProb	Compute prior probability of sequence using Markov model
selex.mmSummary	Summarize Markov model properties
selex.revcomp	Create forward-reverse complement data pairs
selex.run	Run a standard SELEX analysis
selex.sample	Create a sample handle
selex.samplePSFM	Construct a diagnostic PSFM for a FASTQ file
selex.sampleSummary	Show samples visible to the current SELEX session
selex.saveAnnotation	Save sample annotations to file
selex.seqfilter	Create a sequence filter
selex.setwd	Set or change the working directory
selex.split	Randomly split a dataset
selex.summary	Display all count table, Markov model, and information gain summaries