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.

AuthorArnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li
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

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

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

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