Package: SELEX 1.39.0

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_1.39.0.tar.gz
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SELEX.pdf |SELEX.html✨
SELEX/json (API)

# Install 'SELEX' in R:
install.packages('SELEX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:SELEX-1.39.0(bioc 3.21)SELEX-1.38.0(bioc 3.20)

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

softwaremotifdiscoverymotifannotationgeneregulationtranscription

4.30 score 8 scripts 217 downloads 80 mentions 29 exports 20 dependencies

Last updated 23 days agofrom:6a0fd9f11d. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winNOTENov 18 2024
R-4.5-linuxNOTENov 18 2024
R-4.4-winNOTENov 18 2024
R-4.4-macNOTENov 18 2024
R-4.3-winOKNov 18 2024
R-4.3-macOKNov 18 2024

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:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6rJavaS4VectorssysUCSC.utilsXVectorzlibbioc

Motif Discovery with SELEX-seq

Rendered fromSELEX.Rnwusingutils::Sweaveon Nov 18 2024.

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