Files in CharlesJB/mpiGadem
de novo motif discovery
DESCRIPTION
NAMESPACE
R/.svn/all-wcprops
R/.svn/entries
R/.svn/prop-base/AllClasses.R.svn-base
R/.svn/prop-base/GADEM.R.svn-base
R/.svn/prop-base/readGademPWMFile.R.svn-base
R/.svn/prop-base/readPWMfile.R.svn-base
R/.svn/prop-base/readTransfacFile.R.svn-base
R/.svn/text-base/AllClasses.R.svn-base
R/.svn/text-base/AllMethods.R.svn-base
R/.svn/text-base/GADEM.R.svn-base
R/.svn/text-base/readGademPWMFile.R.svn-base
R/.svn/text-base/readPWMfile.R.svn-base
R/.svn/text-base/readTransfacFile.R.svn-base
R/.svn/text-base/zzz.R.svn-base
R/AllClasses.R
R/AllMethods.R
R/GADEM.R
R/readGademPWMFile.R
R/readPWMfile.R
R/readTransfacFile.R
R/zzz.R
README
config.log
config.status
configure
configure.ac
configure.win
inst/.svn/all-wcprops
inst/.svn/entries
inst/doc/.nfs0000000001429c6e00000174
inst/doc/.svn/all-wcprops
inst/doc/.svn/entries
inst/doc/.svn/prop-base/rGADEM.Rnw.svn-base
inst/doc/.svn/prop-base/rGADEM.pdf.svn-base
inst/doc/.svn/text-base/.nfs0000000001429c6e00000174.svn-base
inst/doc/.svn/text-base/rGADEM.Rnw.svn-base
inst/doc/.svn/text-base/rGADEM.pdf.svn-base
inst/doc/rGADEM.Rnw
inst/doc/rGADEM.pdf
inst/extdata/.svn/all-wcprops
inst/extdata/.svn/entries
inst/extdata/.svn/prop-base/Test_100.bed.svn-base
inst/extdata/.svn/text-base/Test_100.bed.svn-base
inst/extdata/.svn/text-base/Test_100.fasta.svn-base
inst/extdata/.svn/text-base/jaspar2009.txt.svn-base
inst/extdata/Test_100.bed
inst/extdata/Test_100.fasta
inst/extdata/jaspar2009.txt
install-sh
man/.svn/all-wcprops
man/.svn/entries
man/.svn/prop-base/GADEM.Rd.svn-base
man/.svn/text-base/GADEM.Rd.svn-base
man/.svn/text-base/align-class.Rd.svn-base
man/.svn/text-base/gadem-class.Rd.svn-base
man/.svn/text-base/motif-class.Rd.svn-base
man/.svn/text-base/parameters-class.Rd.svn-base
man/.svn/text-base/readPWMfile.Rd.svn-base
man/GADEM.Rd
man/align-class.Rd
man/gadem-class.Rd
man/motif-class.Rd
man/parameters-class.Rd
man/readPWMfile.Rd
src/.svn/all-wcprops
src/.svn/entries
src/.svn/prop-base/Gadem_Analysis.c.svn-base
src/.svn/prop-base/Makevars.in.svn-base
src/.svn/prop-base/align_sites.c.svn-base
src/.svn/prop-base/alloc.c.svn-base
src/.svn/prop-base/alloc.h.svn-base
src/.svn/prop-base/base_frequency.c.svn-base
src/.svn/prop-base/check_convergence.c.svn-base
src/.svn/prop-base/check_pwm_dist.c.svn-base
src/.svn/prop-base/consensus.c.svn-base
src/.svn/prop-base/construct_pwm.c.svn-base
src/.svn/prop-base/copy_pwm.c.svn-base
src/.svn/prop-base/crossover.c.svn-base
src/.svn/prop-base/defines.h.svn-base
src/.svn/prop-base/effect_seq_len.c.svn-base
src/.svn/prop-base/evalue_meme.c.svn-base
src/.svn/prop-base/evalue_meme.h.svn-base
src/.svn/prop-base/extend_alignment.c.svn-base
src/.svn/prop-base/gadem.h.svn-base
src/.svn/prop-base/initial_population.c.svn-base
src/.svn/prop-base/mask_sites.c.svn-base
src/.svn/prop-base/mutation.c.svn-base
src/.svn/prop-base/normalization.c.svn-base
src/.svn/prop-base/output.c.svn-base
src/.svn/prop-base/pwm_score_distr.c.svn-base
src/.svn/prop-base/random.h.svn-base
src/.svn/prop-base/read_matrix.c.svn-base
src/.svn/prop-base/read_seq.c.svn-base
src/.svn/prop-base/reverse_seq.c.svn-base
src/.svn/prop-base/sample_wo_replacement.c.svn-base
src/.svn/prop-base/scan_sites.c.svn-base
src/.svn/prop-base/score_subsequence.c.svn-base
src/.svn/prop-base/selection.c.svn-base
src/.svn/prop-base/sort.c.svn-base
src/.svn/prop-base/top_kmers.c.svn-base
src/.svn/prop-base/transform_pwm.c.svn-base
src/.svn/prop-base/weights.c.svn-base
src/.svn/text-base/Gadem_Analysis.c.svn-base
src/.svn/text-base/Makevars.in.svn-base
src/.svn/text-base/Makevars.svn-base
src/.svn/text-base/Makevars.win.in.svn-base
src/.svn/text-base/align_sites.c.svn-base
src/.svn/text-base/alloc.c.svn-base
src/.svn/text-base/alloc.h.svn-base
src/.svn/text-base/background.c.svn-base
src/.svn/text-base/base_frequency.c.svn-base
src/.svn/text-base/check_convergence.c.svn-base
src/.svn/text-base/check_pwm_dist.c.svn-base
src/.svn/text-base/config.h.in.svn-base
src/.svn/text-base/config.h.svn-base
src/.svn/text-base/consensus.c.svn-base
src/.svn/text-base/construct_pwm.c.svn-base
src/.svn/text-base/copy_pwm.c.svn-base
src/.svn/text-base/crossover.c.svn-base
src/.svn/text-base/defines.h.svn-base
src/.svn/text-base/effect_seq_len.c.svn-base
src/.svn/text-base/evalue_meme.c.svn-base
src/.svn/text-base/evalue_meme.h.svn-base
src/.svn/text-base/extend_alignment.c.svn-base
src/.svn/text-base/gadem.h.svn-base
src/.svn/text-base/initial_population.c.svn-base
src/.svn/text-base/mask_sites.c.svn-base
src/.svn/text-base/mpiFunctions.c.svn-base
src/.svn/text-base/mutation.c.svn-base
src/.svn/text-base/normalization.c.svn-base
src/.svn/text-base/output.c.svn-base
src/.svn/text-base/populationCalculation.c.svn-base
src/.svn/text-base/pwm_score_distr.c.svn-base
src/.svn/text-base/random.h.svn-base
src/.svn/text-base/read_matrix.c.svn-base
src/.svn/text-base/read_pwm0.c.svn-base
src/.svn/text-base/read_seq.c.svn-base
src/.svn/text-base/reverse_seq.c.svn-base
src/.svn/text-base/sample_wo_replacement.c.svn-base
src/.svn/text-base/scan_sites.c.svn-base
src/.svn/text-base/score_subsequence.c.svn-base
src/.svn/text-base/selection.c.svn-base
src/.svn/text-base/sort.c.svn-base
src/.svn/text-base/top_kmers.c.svn-base
src/.svn/text-base/transform_pwm.c.svn-base
src/.svn/text-base/weights.c.svn-base
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/mpiFunctions.c
src/mutation.c
src/normalization.c
src/output.c
src/populationCalculation.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
trunk/.svn/all-wcprops
trunk/.svn/entries
trunk/.svn/prop-base/configure.svn-base
trunk/.svn/text-base/configure.svn-base
trunk/DESCRIPTION
trunk/NAMESPACE
trunk/R/.svn/all-wcprops
trunk/R/.svn/entries
trunk/R/.svn/prop-base/AllClasses.R.svn-base
trunk/R/.svn/prop-base/GADEM.R.svn-base
trunk/R/.svn/prop-base/readGademPWMFile.R.svn-base
trunk/R/.svn/prop-base/readPWMfile.R.svn-base
trunk/R/.svn/prop-base/readTransfacFile.R.svn-base
trunk/R/.svn/text-base/AllClasses.R.svn-base
trunk/R/.svn/text-base/AllMethods.R.svn-base
trunk/R/.svn/text-base/GADEM.R.svn-base
trunk/R/.svn/text-base/readGademPWMFile.R.svn-base
trunk/R/.svn/text-base/readPWMfile.R.svn-base
trunk/R/.svn/text-base/readTransfacFile.R.svn-base
trunk/R/.svn/text-base/zzz.R.svn-base
trunk/R/AllClasses.R
trunk/R/AllMethods.R
trunk/R/GADEM.R
trunk/R/readGademPWMFile.R
trunk/R/readPWMfile.R
trunk/R/readTransfacFile.R
trunk/R/zzz.R
trunk/config.log
trunk/config.status
trunk/configure
trunk/configure.ac
trunk/configure.win
trunk/inst/.svn/all-wcprops
trunk/inst/.svn/entries
trunk/inst/doc/.nfs0000000001429c6e00000174
trunk/inst/doc/.svn/all-wcprops
trunk/inst/doc/.svn/entries
trunk/inst/doc/.svn/prop-base/rGADEM.Rnw.svn-base
trunk/inst/doc/.svn/prop-base/rGADEM.pdf.svn-base
trunk/inst/doc/.svn/text-base/.nfs0000000001429c6e00000174.svn-base
trunk/inst/doc/.svn/text-base/rGADEM.Rnw.svn-base
trunk/inst/doc/.svn/text-base/rGADEM.pdf.svn-base
trunk/inst/doc/rGADEM.Rnw
trunk/inst/doc/rGADEM.pdf
trunk/inst/extdata/.svn/all-wcprops
trunk/inst/extdata/.svn/entries
trunk/inst/extdata/.svn/prop-base/Test_100.bed.svn-base
trunk/inst/extdata/.svn/text-base/Test_100.bed.svn-base
trunk/inst/extdata/.svn/text-base/Test_100.fasta.svn-base
trunk/inst/extdata/.svn/text-base/jaspar2009.txt.svn-base
trunk/inst/extdata/Test_100.bed
trunk/inst/extdata/Test_100.fasta
trunk/inst/extdata/jaspar2009.txt
trunk/install-sh
trunk/man/.svn/all-wcprops
trunk/man/.svn/entries
trunk/man/.svn/prop-base/GADEM.Rd.svn-base
trunk/man/.svn/text-base/GADEM.Rd.svn-base
trunk/man/.svn/text-base/align-class.Rd.svn-base
trunk/man/.svn/text-base/gadem-class.Rd.svn-base
trunk/man/.svn/text-base/motif-class.Rd.svn-base
trunk/man/.svn/text-base/parameters-class.Rd.svn-base
trunk/man/.svn/text-base/readPWMfile.Rd.svn-base
trunk/man/GADEM.Rd
trunk/man/align-class.Rd
trunk/man/gadem-class.Rd
trunk/man/motif-class.Rd
trunk/man/parameters-class.Rd
trunk/man/readPWMfile.Rd
trunk/src/.svn/all-wcprops
trunk/src/.svn/entries
trunk/src/.svn/prop-base/Gadem_Analysis.c.svn-base
trunk/src/.svn/prop-base/Makevars.in.svn-base
trunk/src/.svn/prop-base/align_sites.c.svn-base
trunk/src/.svn/prop-base/alloc.c.svn-base
trunk/src/.svn/prop-base/alloc.h.svn-base
trunk/src/.svn/prop-base/base_frequency.c.svn-base
trunk/src/.svn/prop-base/check_convergence.c.svn-base
trunk/src/.svn/prop-base/check_pwm_dist.c.svn-base
trunk/src/.svn/prop-base/consensus.c.svn-base
trunk/src/.svn/prop-base/construct_pwm.c.svn-base
trunk/src/.svn/prop-base/copy_pwm.c.svn-base
trunk/src/.svn/prop-base/crossover.c.svn-base
trunk/src/.svn/prop-base/defines.h.svn-base
trunk/src/.svn/prop-base/effect_seq_len.c.svn-base
trunk/src/.svn/prop-base/evalue_meme.c.svn-base
trunk/src/.svn/prop-base/evalue_meme.h.svn-base
trunk/src/.svn/prop-base/extend_alignment.c.svn-base
trunk/src/.svn/prop-base/gadem.h.svn-base
trunk/src/.svn/prop-base/initial_population.c.svn-base
trunk/src/.svn/prop-base/mask_sites.c.svn-base
trunk/src/.svn/prop-base/mutation.c.svn-base
trunk/src/.svn/prop-base/normalization.c.svn-base
trunk/src/.svn/prop-base/output.c.svn-base
trunk/src/.svn/prop-base/pwm_score_distr.c.svn-base
trunk/src/.svn/prop-base/random.h.svn-base
trunk/src/.svn/prop-base/read_matrix.c.svn-base
trunk/src/.svn/prop-base/read_seq.c.svn-base
trunk/src/.svn/prop-base/reverse_seq.c.svn-base
trunk/src/.svn/prop-base/sample_wo_replacement.c.svn-base
trunk/src/.svn/prop-base/scan_sites.c.svn-base
trunk/src/.svn/prop-base/score_subsequence.c.svn-base
trunk/src/.svn/prop-base/selection.c.svn-base
trunk/src/.svn/prop-base/sort.c.svn-base
trunk/src/.svn/prop-base/top_kmers.c.svn-base
trunk/src/.svn/prop-base/transform_pwm.c.svn-base
trunk/src/.svn/prop-base/weights.c.svn-base
trunk/src/.svn/text-base/Gadem_Analysis.c.svn-base
trunk/src/.svn/text-base/Makevars.in.svn-base
trunk/src/.svn/text-base/Makevars.svn-base
trunk/src/.svn/text-base/Makevars.win.in.svn-base
trunk/src/.svn/text-base/align_sites.c.svn-base
trunk/src/.svn/text-base/alloc.c.svn-base
trunk/src/.svn/text-base/alloc.h.svn-base
trunk/src/.svn/text-base/background.c.svn-base
trunk/src/.svn/text-base/base_frequency.c.svn-base
trunk/src/.svn/text-base/check_convergence.c.svn-base
trunk/src/.svn/text-base/check_pwm_dist.c.svn-base
trunk/src/.svn/text-base/config.h.in.svn-base
trunk/src/.svn/text-base/config.h.svn-base
trunk/src/.svn/text-base/consensus.c.svn-base
trunk/src/.svn/text-base/construct_pwm.c.svn-base
trunk/src/.svn/text-base/copy_pwm.c.svn-base
trunk/src/.svn/text-base/crossover.c.svn-base
trunk/src/.svn/text-base/defines.h.svn-base
trunk/src/.svn/text-base/effect_seq_len.c.svn-base
trunk/src/.svn/text-base/evalue_meme.c.svn-base
trunk/src/.svn/text-base/evalue_meme.h.svn-base
trunk/src/.svn/text-base/extend_alignment.c.svn-base
trunk/src/.svn/text-base/gadem.h.svn-base
trunk/src/.svn/text-base/initial_population.c.svn-base
trunk/src/.svn/text-base/mask_sites.c.svn-base
trunk/src/.svn/text-base/mpiFunctions.c.svn-base
trunk/src/.svn/text-base/mutation.c.svn-base
trunk/src/.svn/text-base/normalization.c.svn-base
trunk/src/.svn/text-base/output.c.svn-base
trunk/src/.svn/text-base/populationCalculation.c.svn-base
trunk/src/.svn/text-base/pwm_score_distr.c.svn-base
trunk/src/.svn/text-base/random.h.svn-base
trunk/src/.svn/text-base/read_matrix.c.svn-base
trunk/src/.svn/text-base/read_pwm0.c.svn-base
trunk/src/.svn/text-base/read_seq.c.svn-base
trunk/src/.svn/text-base/reverse_seq.c.svn-base
trunk/src/.svn/text-base/sample_wo_replacement.c.svn-base
trunk/src/.svn/text-base/scan_sites.c.svn-base
trunk/src/.svn/text-base/score_subsequence.c.svn-base
trunk/src/.svn/text-base/selection.c.svn-base
trunk/src/.svn/text-base/sort.c.svn-base
trunk/src/.svn/text-base/top_kmers.c.svn-base
trunk/src/.svn/text-base/transform_pwm.c.svn-base
trunk/src/.svn/text-base/weights.c.svn-base
trunk/src/Gadem_Analysis.c
trunk/src/Makevars
trunk/src/Makevars.in
trunk/src/Makevars.win.in
trunk/src/align_sites.c
trunk/src/alloc.c
trunk/src/alloc.h
trunk/src/background.c
trunk/src/base_frequency.c
trunk/src/check_convergence.c
trunk/src/check_pwm_dist.c
trunk/src/config.h
trunk/src/config.h.in
trunk/src/consensus.c
trunk/src/construct_pwm.c
trunk/src/copy_pwm.c
trunk/src/crossover.c
trunk/src/defines.h
trunk/src/effect_seq_len.c
trunk/src/evalue_meme.c
trunk/src/evalue_meme.h
trunk/src/extend_alignment.c
trunk/src/gadem.h
trunk/src/initial_population.c
trunk/src/mask_sites.c
trunk/src/mpiFunctions.c
trunk/src/mutation.c
trunk/src/normalization.c
trunk/src/output.c
trunk/src/populationCalculation.c
trunk/src/pwm_score_distr.c
trunk/src/random.h
trunk/src/read_matrix.c
trunk/src/read_pwm0.c
trunk/src/read_seq.c
trunk/src/reverse_seq.c
trunk/src/sample_wo_replacement.c
trunk/src/scan_sites.c
trunk/src/score_subsequence.c
trunk/src/selection.c
trunk/src/sort.c
trunk/src/top_kmers.c
trunk/src/transform_pwm.c
trunk/src/weights.c
