Files in bjmt/universalmotif
Import, Modify, and Export Motifs with R
.Rbuildignore
DESCRIPTION
Makefile
NAMESPACE
NEWS
R/RcppExports.R
R/add_multifreq.R
R/compare_motifs.R
R/convert_motifs.R
R/convert_type.R
R/create_motif.R
R/create_sequences.R
R/data.R
R/enrich_motifs.R
R/filter_motifs.R
R/get_bkg.R
R/make_DBscores.R
R/merge_motifs.R
R/merge_similar.R
R/motif_clusters.R
R/motif_finder.R
R/motif_peaks.R
R/motif_pvalue.R
R/motif_rc.R
R/motif_tree.R
R/read_cisbp.R
R/read_homer.R
R/read_jaspar.R
R/read_matrix.R
R/read_meme.R
R/read_motifs.R
R/read_transfac.R
R/read_uniprobe.R
R/run_meme.R
R/sample_sites.R
R/scan_sequences.R
R/sequence_complexity.R
R/shuffle_motifs.R
R/shuffle_sequences.R
R/switch_alph.R
R/trim_motifs.R
R/universalmotif-class.R
R/universalmotif-methods.R
R/universalmotif.R
R/universalmotif_df.R
R/utils-internal.R
R/utils-motif.R
R/utils-sequence.R
R/view_logo.R
R/view_motifs.R
R/write_homer.R
R/write_jaspar.R
R/write_matrix.R
R/write_meme.R
R/write_motifs.R
R/write_transfac.R
R/zzz.R
README.md
data/ArabidopsisMotif.rda
data/ArabidopsisPromoters.rda
data/JASPAR2018_CORE_DBSCORES.rda
data/examplemotif.rda
data/examplemotif2.rda
data/fontDFroboto.rda
inst/extdata/cisbp.txt
inst/extdata/dreme.txt
inst/extdata/hocomoco.txt
inst/extdata/homer.txt
inst/extdata/jaspar.txt
inst/extdata/meme_custom_alph.txt
inst/extdata/meme_full.txt
inst/extdata/meme_minimal.txt
inst/extdata/sites.txt
inst/extdata/transfac.txt
inst/extdata/uniprobe_full.txt
inst/extdata/uniprobe_minimal.txt
inst/extdata/universalmotif.txt
inst/figures/example1.png
inst/figures/example2.png
man/ArabidopsisMotif.Rd
man/ArabidopsisPromoters.Rd
man/JASPAR2018_CORE_DBSCORES.Rd
man/add_multifreq.Rd
man/compare_motifs.Rd
man/convert_motifs.Rd
man/convert_type.Rd
man/create_motif.Rd
man/create_sequences.Rd
man/enrich_motifs.Rd
man/examplemotif.Rd
man/examplemotif2.Rd
man/filter_motifs.Rd
man/fontDFroboto.Rd
man/get_bkg.Rd
man/make_DBscores.Rd
man/merge_motifs.Rd
man/merge_similar.Rd
man/motif_peaks.Rd
man/motif_pvalue.Rd
man/motif_rc.Rd
man/motif_tree.Rd
man/read_cisbp.Rd
man/read_homer.Rd
man/read_jaspar.Rd
man/read_matrix.Rd
man/read_meme.Rd
man/read_motifs.Rd
man/read_transfac.Rd
man/read_uniprobe.Rd
man/reexports.Rd
man/run_meme.Rd
man/sample_sites.Rd
man/scan_sequences.Rd
man/sequence_complexity.Rd
man/shuffle_motifs.Rd
man/shuffle_sequences.Rd
man/switch_alph.Rd
man/tidy-motifs.Rd
man/trim_motifs.Rd
man/universalmotif-class.Rd
man/universalmotif-pkg.Rd
man/utilities.Rd
man/utils-motif.Rd
man/utils-sequence.Rd
man/view_logo.Rd
man/view_motifs.Rd
man/write_homer.Rd
man/write_jaspar.Rd
man/write_matrix.Rd
man/write_meme.Rd
man/write_motifs.Rd
man/write_transfac.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/add_multifreq.cpp
src/calc_complexity.cpp
src/compare_motifs.cpp
src/get_bkg.cpp
src/motif_finder.cpp
src/motif_peaks.cpp
src/motif_pvalue.cpp
src/scan_sequences.cpp
src/shuffle_sequences.cpp
src/shuffle_sequences.h
src/trim_motifs.cpp
src/types.h
src/universalmotif-class.cpp
src/utils-exported.cpp
src/utils-exported.h
src/utils-internal.cpp
src/utils-internal.h
tests/spelling.R
tests/testthat.R
tests/testthat/test_add_multifreq.R
tests/testthat/test_compare_motifs.R
tests/testthat/test_convert_motifs.R
tests/testthat/test_convert_type.R
tests/testthat/test_create_motif.R
tests/testthat/test_create_sequences.R
tests/testthat/test_enrich_motifs.R
tests/testthat/test_filter_motifs.R
tests/testthat/test_get_bkg.R
tests/testthat/test_merge_motifs.R
tests/testthat/test_motif_peaks.R
tests/testthat/test_motif_pvalue.R
tests/testthat/test_motif_rc.R
tests/testthat/test_motif_tree.R
tests/testthat/test_read_motifs.R
tests/testthat/test_run_meme.R
tests/testthat/test_sample_sites.R
tests/testthat/test_scan_sequences.R
tests/testthat/test_shuffle_motifs.R
tests/testthat/test_shuffle_sequences.R
tests/testthat/test_switch_alph.R
tests/testthat/test_trim_motifs.R
tests/testthat/test_universalmotif-methods.R
tests/testthat/test_universalmotif_df.R
tests/testthat/test_utils.R
tests/testthat/test_view_motifs.R
tests/testthat/test_write_motifs.R
todo
vignettes/Introduction.Rmd
vignettes/IntroductionToSequenceMotifs.Rmd
vignettes/MotifComparisonAndPvalues.Rmd
vignettes/MotifManipulation.Rmd
vignettes/SequenceSearches.Rmd
vignettes/universalmotif.bib
