SELEX: Functions for analyzing SELEX-seq data

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SELEX")
AuthorChaitanya Rastogi, Dahong Liu, and Harmen Bussemaker
Bioconductor views GeneRegulation MotifAnnotation MotifDiscovery Software Transcription
Date of publicationNone
MaintainerHarmen Bussemaker <hjb2004@columbia.edu>
LicenseGPL (>=2)
Version1.8.0
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...

Functions

selex Man page
Selex Man page
selex.affinities Man page
selex.config Man page
selex.counts Man page
selex.countSummary Man page
selex.defineSample Man page
selex.exampledata Man page
selex.fastqPSFM Man page
selex.getAttributes Man page
selex.getRound0 Man page
selex.getSeqfilter Man page
selex.infogain Man page
selex.infogainSummary Man page
selex.jvmStatus Man page
selex.kmax Man page
selex.kmerPSFM Man page
selex.loadAnnotation Man page
selex.mm Man page
selex.mmProb Man page
selex.mmSummary Man page
SELEX-package Man page
selex.revcomp Man page
selex.run Man page
selex.sample Man page
selex.samplePSFM Man page
selex.sampleSummary Man page
selex.saveAnnotation Man page
selex.seqfilter Man page
selex.setwd Man page
selex.split Man page
selex.summary Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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