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SELEX (version 1.4.0)

Functions for analyzing SELEX-seq data

Description

Tools for quantifying DNA binding specificities based on SELEX-seq data

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Version

Version

1.4.0

License

GPL (>=2)

Maintainer

Harmen Bussemaker

Last Published

February 15th, 2017

Functions in SELEX (1.4.0)

selex.mmProb

Compute prior probability of sequence using Markov model
selex.config

Set SELEX system parameters
selex.kmax

Calculate kmax for a dataset
selex.infogainSummary

Summarize available information gain values
SELEX

SELEX Package
selex.getSeqfilter

Display sequence filter attributes
selex.samplePSFM

Construct a diagnostic PSFM for a FASTQ file
selex.summary

Display all count table, Markov model, and information gain summaries
selex.mmSummary

Summarize Markov model properties
selex.exampledata

Extract example data files
selex.run

Run a standard SELEX analysis
selex.fastqPSFM

Construct a diagnostic PSFM for a FASTQ file
selex.saveAnnotation

Save sample annotations to file
selex.split

Randomly split a dataset
selex.sample

Create a sample handle
selex.counts

Construct or retrieve a K-mer count table
selex.sampleSummary

Show samples visible to the current SELEX session
selex.seqfilter

Create a sequence filter
selex.getRound0

Obtain round zero sample handle
selex.revcomp

Create forward-reverse complement data pairs
selex.jvmStatus

Display current JVM memory usage
selex.loadAnnotation

Load a sample annotation file
selex.affinities

Construct a K-mer affinity table
selex.setwd

Set or change the working directory
selex.infogain

Compute or retrieve information gain between rounds
selex.getAttributes

Display sample handle properties
selex.kmerPSFM

Construct a PSFM from a K-mer table
selex.defineSample

Define annotation for an individual sample
selex.countSummary

Summarize available K-mer count tables
selex.mm

Build or retrieve a Markov model