SELEX: Functions for analyzing SELEX-seq data

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

AuthorChaitanya Rastogi, Dahong Liu, and Harmen Bussemaker
Date of publicationNone
MaintainerHarmen Bussemaker <hjb2004@columbia.edu>
LicenseGPL (>=2)
Version1.6.0
http://bussemakerlab.org/software/SELEX/

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

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