SELEX: Functions for analyzing SELEX-seq data

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

Author
Chaitanya Rastogi, Dahong Liu, and Harmen Bussemaker
Date of publication
None
Maintainer
Harmen Bussemaker <hjb2004@columbia.edu>
License
GPL (>=2)
Version
1.6.0
URLs

View on Bioconductor

Man pages

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...

Files in this package

SELEX/DESCRIPTION
SELEX/NAMESPACE
SELEX/R
SELEX/R/SELEX.R
SELEX/R/onLoad.R
SELEX/build
SELEX/build/vignette.rds
SELEX/inst
SELEX/inst/doc
SELEX/inst/doc/SELEX.R
SELEX/inst/doc/SELEX.Rnw
SELEX/inst/doc/SELEX.pdf
SELEX/inst/extdata
SELEX/inst/extdata/R0.fastq.gz
SELEX/inst/extdata/R2.fastq.gz
SELEX/inst/extdata/config.xml
SELEX/inst/java
SELEX/inst/java/selex.jar
SELEX/java
SELEX/java/src
SELEX/java/src/Makefile
SELEX/java/src/base
SELEX/java/src/base/ArraysMerger.java
SELEX/java/src/base/ArraysMergerHeap.java
SELEX/java/src/base/CountObject.java
SELEX/java/src/base/CountObjectIterator.java
SELEX/java/src/base/DebugLog.java
SELEX/java/src/base/FatalException.java
SELEX/java/src/base/MarkovModelInfo.java
SELEX/java/src/base/MarkovModelOption.java
SELEX/java/src/base/QuickSort.java
SELEX/java/src/base/RegexOption.java
SELEX/java/src/base/SELEXConfigReader.java
SELEX/java/src/base/Sequence.java
SELEX/java/src/base/SequenceComparator.java
SELEX/java/src/base/Util.java
SELEX/java/src/data
SELEX/java/src/data/selex
SELEX/java/src/data/selex/filelist
SELEX/java/src/main
SELEX/java/src/main/CountFileReader.java
SELEX/java/src/main/FastQFileScanner.java
SELEX/java/src/main/SELEX.java
SELEX/java/src/main/SELEXConfigGUI.java
SELEX/java/src/main/SampleDataFileExtractor.java
SELEX/java/src/main/SimpleKmerCount.java
SELEX/java/src/selex.jar
SELEX/java/src/selex.xsd
SELEX/java/src/test
SELEX/java/src/test/CountFileReaderTest.java
SELEX/java/src/test/ExecutorTest.java
SELEX/java/src/test/IntegerHolder.java
SELEX/java/src/test/Kmer.java
SELEX/java/src/test/MappedMemTest.java
SELEX/java/src/test/MinHeap.java
SELEX/java/src/test/MinHeapTest.java
SELEX/java/src/test/RadixSortTest.java
SELEX/java/src/test/RegTest.java
SELEX/java/src/test/SELEXTest1.java
SELEX/java/src/test/SELEXTest2.java
SELEX/java/src/test/SequenceTest.java
SELEX/java/src/test/Sorting.java
SELEX/java/src/test/SortingTest.java
SELEX/java/src/test/UtilTest.java
SELEX/java/src/test/ZipfileTest.java
SELEX/man
SELEX/man/SELEX.Rd
SELEX/man/selex.affinities.Rd
SELEX/man/selex.config.Rd
SELEX/man/selex.countSummary.Rd
SELEX/man/selex.counts.Rd
SELEX/man/selex.defineSample.Rd
SELEX/man/selex.exampledata.Rd
SELEX/man/selex.fastqPSFM.Rd
SELEX/man/selex.getAttributes.Rd
SELEX/man/selex.getRound0.Rd
SELEX/man/selex.getSeqfilter.Rd
SELEX/man/selex.infogain.Rd
SELEX/man/selex.infogainSummary.Rd
SELEX/man/selex.jvmStatus.Rd
SELEX/man/selex.kmax.Rd
SELEX/man/selex.kmerPSFM.Rd
SELEX/man/selex.loadAnnotation.Rd
SELEX/man/selex.mm.Rd
SELEX/man/selex.mmProb.Rd
SELEX/man/selex.mmSummary.Rd
SELEX/man/selex.revcomp.Rd
SELEX/man/selex.run.Rd
SELEX/man/selex.sample.Rd
SELEX/man/selex.samplePSFM.Rd
SELEX/man/selex.sampleSummary.Rd
SELEX/man/selex.saveAnnotation.Rd
SELEX/man/selex.seqfilter.Rd
SELEX/man/selex.setwd.Rd
SELEX/man/selex.split.Rd
SELEX/man/selex.summary.Rd
SELEX/vignettes
SELEX/vignettes/SELEX.Rnw