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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rGADEM")
AuthorArnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li
Bioconductor views ChIPSeq ChIPchip Microarray MotifDiscovery Sequencing
Date of publicationNone
MaintainerArnaud Droit <arnaud.droit@crchuq.ulaval.ca>
LicenseArtistic-2.0
Version2.22.0

View on Bioconductor

Functions

align Man page
align-class Man page
consensus Man page
consensus,gadem-method Man page
dim,gadem-method Man page
endPos Man page
endPos,gadem-method Man page
gadem Man page
GADEM Man page
[,gadem,ANY,ANY-method Man page
[[,gadem,ANY,ANY-method Man page
gadem-class Man page
[,gadem-method Man page
[[,gadem-method Man page
getPWM Man page
getPWM,gadem-method Man page
getPWM,motif-method Man page
length,gadem-method Man page
motif Man page
motif-class Man page
names<-,gadem-method Man page
names,gadem-method Man page
nMotifs Man page
nMotifs,gadem-method Man page
nOccurrences Man page
nOccurrences,gadem-method Man page
parameters Man page
parameters-class Man page
parameters,gadem-method Man page
plot,gadem,ANY-method Man page
plot,gadem-method Man page
plot,motif,ANY-method Man page
readPWMfile Man page
startPos Man page
startPos,gadem-method Man page
summary,list-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllMethods.R R/GADEM.R R/readGademPWMFile.R R/readPWMfile.R R/readTransfacFile.R R/zzz.R
build
build/vignette.rds
configure
configure.ac
configure.win
inst
inst/doc
inst/doc/rGADEM.R
inst/doc/rGADEM.Rnw
inst/doc/rGADEM.pdf
inst/extdata
inst/extdata/Test_100.bed
inst/extdata/Test_100.fasta
inst/extdata/jaspar2009.txt
install-sh
man
man/GADEM.Rd man/align-class.Rd man/gadem-class.Rd man/motif-class.Rd man/parameters-class.Rd man/readPWMfile.Rd
src
src/Gadem_Analysis.c
src/Makevars
src/Makevars.in
src/Makevars.win.in
src/align_sites.c
src/alloc.c
src/alloc.h
src/background.c
src/base_frequency.c
src/check_convergence.c
src/check_pwm_dist.c
src/config.h
src/config.h.in
src/consensus.c
src/construct_pwm.c
src/copy_pwm.c
src/crossover.c
src/defines.h
src/effect_seq_len.c
src/evalue_meme.c
src/evalue_meme.h
src/extend_alignment.c
src/gadem.h
src/initial_population.c
src/mask_sites.c
src/mutation.c
src/normalization.c
src/output.c
src/pwm_score_distr.c
src/random.h
src/read_matrix.c
src/read_pwm0.c
src/read_seq.c
src/reverse_seq.c
src/sample_wo_replacement.c
src/scan_sites.c
src/score_subsequence.c
src/selection.c
src/sort.c
src/top_kmers.c
src/transform_pwm.c
src/weights.c
vignettes
vignettes/rGADEM.Rnw

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.