Package: rGADEM 2.55.0

Arnaud Droit

rGADEM: de novo motif discovery

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.

Authors:Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li

rGADEM_2.55.0.tar.gz
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rGADEM.pdf |rGADEM.html✨
rGADEM/json (API)

# Install 'rGADEM' in R:

install.packages('rGADEM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openmp– GCC OpenMP (GOMP) support library

On BioConductor:rGADEM-2.55.0(bioc 3.21)rGADEM-2.54.0(bioc 3.20)

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

microarray chipchip sequencing chipseq motifdiscovery openmp

4.95 score 56 scripts 686 downloads 8 mentions 10 exports 52 dependencies

Last updated 2 months agofrom:0bdc9ac352. Checks:OK: 1 WARNING: 5 NOTE: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win-x86_64	WARNING	Dec 18 2024
R-4.5-linux-x86_64	WARNING	Dec 18 2024
R-4.4-win-x86_64	WARNING	Dec 18 2024
R-4.4-mac-x86_64	WARNING	Dec 18 2024
R-4.4-mac-aarch64	WARNING	Dec 18 2024
R-4.3-win-x86_64	NOTE	Dec 18 2024
R-4.3-mac-x86_64	NOTE	Dec 18 2024
R-4.3-mac-aarch64	NOTE	Dec 18 2024

Exports:consensus endPos GADEM getPWM nMotifs nOccurrences parameters plot readPWMfile startPos

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors seqLogo snow SparseArray SummarizedExperiment sys UCSC.utils XML XVector yaml zlibbioc

The rGADEM users guide

Rendered fromrGADEM.Rnwusingutils::Sweaveon Dec 18 2024.

Last update: 2019-12-16
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class "align"	align align-class
Motif Analysis with rGADEM	GADEM
Class "gadem"	consensus consensus,gadem-method dim,gadem-method endPos endPos,gadem-method gadem gadem-class getPWM getPWM,gadem-method getPWM,motif-method length,gadem-method names,gadem-method names<-,gadem-method nMotifs,gadem-method nOccurrences nOccurrences,gadem-method parameters,gadem-method plot,gadem,ANY-method plot,gadem-method plot,motif,ANY-method startPos startPos,gadem-method summary,list-method [,gadem,ANY,ANY,ANY-method [,gadem,ANY,ANY-method [,gadem-method [[,gadem,ANY,ANY-method [[,gadem-method
Class "motif"	motif motif-class nMotifs
Class "parameters"	parameters parameters-class
Read Transfac File	readPWMfile