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.

Author
Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li
Date of publication
None
Maintainer
Arnaud Droit <arnaud.droit@crchuq.ulaval.ca>
License
Artistic-2.0
Version
2.22.0

View on Bioconductor

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

Files in this package

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