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✨
DESCRIPTION
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.

software motifdiscovery motifannotation generegulation transcription openjdk

4.41 score 13 scripts 80 mentions 29 exports 9 dependencies

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

Target	Result	Time
bioc-checks	ERROR	153
linux-devel-x86_64	NOTE	220
source / vignettes	OK	207
linux-release-x86_64	NOTE	293
macos-release-arm64	NOTE	128
macos-oldrel-arm64	NOTE	135
windows-devel	NOTE	129
windows-release	NOTE	133
windows-oldrel	NOTE	178
wasm-release	OK	102

Exports:selex.affinities selex.config selex.counts selex.countSummary selex.defineSample selex.exampledata selex.fastqPSFM selex.getAttributes selex.getRound0 selex.getSeqfilter selex.infogain selex.infogainSummary selex.jvmStatus selex.kmax selex.kmerPSFM selex.loadAnnotation selex.mm selex.mmProb selex.mmSummary selex.revcomp selex.run selex.sample selex.samplePSFM selex.sampleSummary selex.saveAnnotation selex.seqfilter selex.setwd selex.split selex.summary

Dependencies:BiocGenerics Biostrings crayon generics IRanges rJava S4Vectors Seqinfo XVector

Motif Discovery with SELEX-seq

Rendered fromSELEX.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SELEX Package	SELEX-package Selex selex
Construct a K-mer affinity table	selex.affinities
Set SELEX system parameters	selex.config
Construct or retrieve a K-mer count table	selex.counts
Summarize available K-mer count tables	selex.countSummary
Define annotation for an individual sample	selex.defineSample
Extract example data files	selex.exampledata
Construct a diagnostic PSFM for a FASTQ file	selex.fastqPSFM
Display sample handle properties	selex.getAttributes
Obtain round zero sample handle	selex.getRound0
Display sequence filter attributes	selex.getSeqfilter
Compute or retrieve information gain between rounds	selex.infogain
Summarize available information gain values	selex.infogainSummary
Display current JVM memory usage	selex.jvmStatus
Calculate kmax for a dataset	selex.kmax
Construct a PSFM from a K-mer table	selex.kmerPSFM
Load a sample annotation file	selex.loadAnnotation
Build or retrieve a Markov model	selex.mm
Compute prior probability of sequence using Markov model	selex.mmProb
Summarize Markov model properties	selex.mmSummary
Create forward-reverse complement data pairs	selex.revcomp
Run a standard SELEX analysis	selex.run
Create a sample handle	selex.sample
Construct a diagnostic PSFM for a FASTQ file	selex.samplePSFM
Show samples visible to the current SELEX session	selex.sampleSummary
Save sample annotations to file	selex.saveAnnotation
Create a sequence filter	selex.seqfilter
Set or change the working directory	selex.setwd
Randomly split a dataset	selex.split
Display all count table, Markov model, and information gain summaries	selex.summary