Package: SELEX 1.45.0

Harmen J. Bussemaker

SELEX: Functions for analyzing SELEX-seq data

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

Authors:Chaitanya Rastogi, Dahong Liu, Lucas Melo, and Harmen J. Bussemaker

SELEX_1.45.0.tar.gz
SELEX_1.45.0.zip(r-4.7)SELEX_1.45.0.zip(r-4.6)SELEX_1.45.0.zip(r-4.5)
SELEX_1.45.0.tgz(r-4.6-any)SELEX_1.45.0.tgz(r-4.5-any)
SELEX_1.45.0.tar.gz(r-4.7-any)SELEX_1.45.0.tar.gz(r-4.6-any)
SELEX_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SELEX/json (API)

# Install 'SELEX' in R:
install.packages('SELEX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:SELEX-1.45.0(bioc 3.24)SELEX-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwaremotifdiscoverymotifannotationgeneregulationtranscriptionopenjdk

4.56 score 18 scripts 402 downloads 80 mentions 29 exports 9 dependencies

Last updated from:1121f3efc0. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR156
linux-devel-x86_64NOTE235
source / vignettesOK206
linux-release-x86_64NOTE234
macos-release-arm64NOTE122
macos-oldrel-arm64NOTE181
windows-develNOTE144
windows-releaseNOTE110
windows-oldrelNOTE123
wasm-releaseOK106

Exports:selex.affinitiesselex.configselex.countsselex.countSummaryselex.defineSampleselex.exampledataselex.fastqPSFMselex.getAttributesselex.getRound0selex.getSeqfilterselex.infogainselex.infogainSummaryselex.jvmStatusselex.kmaxselex.kmerPSFMselex.loadAnnotationselex.mmselex.mmProbselex.mmSummaryselex.revcompselex.runselex.sampleselex.samplePSFMselex.sampleSummaryselex.saveAnnotationselex.seqfilterselex.setwdselex.splitselex.summary

Dependencies:BiocGenericsBiostringscrayongenericsIRangesrJavaS4VectorsSeqinfoXVector

Motif Discovery with SELEX-seq

Rendered fromSELEX.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2015-02-28
Started: 2015-02-28

Readme and manuals

Help Manual

Help pageTopics
SELEX PackageSELEX-package Selex selex
Construct a K-mer affinity tableselex.affinities
Set SELEX system parametersselex.config
Construct or retrieve a K-mer count tableselex.counts
Summarize available K-mer count tablesselex.countSummary
Define annotation for an individual sampleselex.defineSample
Extract example data filesselex.exampledata
Construct a diagnostic PSFM for a FASTQ fileselex.fastqPSFM
Display sample handle propertiesselex.getAttributes
Obtain round zero sample handleselex.getRound0
Display sequence filter attributesselex.getSeqfilter
Compute or retrieve information gain between roundsselex.infogain
Summarize available information gain valuesselex.infogainSummary
Display current JVM memory usageselex.jvmStatus
Calculate kmax for a datasetselex.kmax
Construct a PSFM from a K-mer tableselex.kmerPSFM
Load a sample annotation fileselex.loadAnnotation
Build or retrieve a Markov modelselex.mm
Compute prior probability of sequence using Markov modelselex.mmProb
Summarize Markov model propertiesselex.mmSummary
Create forward-reverse complement data pairsselex.revcomp
Run a standard SELEX analysisselex.run
Create a sample handleselex.sample
Construct a diagnostic PSFM for a FASTQ fileselex.samplePSFM
Show samples visible to the current SELEX sessionselex.sampleSummary
Save sample annotations to fileselex.saveAnnotation
Create a sequence filterselex.seqfilter
Set or change the working directoryselex.setwd
Randomly split a datasetselex.split
Display all count table, Markov model, and information gain summariesselex.summary