rGADEM: de novo motif discovery
Version 2.24.0

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.

Browse man pages Browse package API and functions Browse package files

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
Version2.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rGADEM")

Man pages

align-class: Class "align"
GADEM: Motif Analysis with rGADEM
gadem-class: Class "gadem"
motif-class: Class "motif"
parameters-class: Class "parameters"
readPWMfile: Read Transfac File

Functions

GADEM Man page Source code
[,gadem,ANY,ANY,ANY-method Man page
[,gadem,ANY,ANY-method Man page
[,gadem-method Man page
[[,gadem,ANY,ANY-method Man page
[[,gadem-method Man page
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-class 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
nMotifs Man page
nMotifs,gadem-method Man page
nOccurrences Man page
nOccurrences,gadem-method Man page
names,gadem-method Man page
names<-,gadem-method Man page
onLoad Source code
parameters Man page
parameters,gadem-method Man page
parameters-class Man page
plot,gadem,ANY-method Man page
plot,gadem-method Man page
plot,motif,ANY-method Man page
readGademPWMFile Source code
readPWMfile Man page Source code
readTransfacFile Source code
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
rGADEM documentation built on May 20, 2017, 10:49 p.m.