Files in universalmotif

Import, Modify, and Export Motifs with R

NEWS

README.md

NAMESPACE

DESCRIPTION

R/RcppExports.R R/read_homer.R R/utils-sequence.R R/read_jaspar.R R/view_motifs.R R/merge_motifs.R R/utils-internal.R R/enrich_motifs.R R/filter_motifs.R R/shuffle_motifs.R R/data.R R/make_DBscores.R R/convert_type.R R/read_motifs.R R/read_meme.R R/write_motifs.R R/scan_sequences.R R/read_uniprobe.R R/add_multifreq.R R/write_homer.R R/motif_tree.R R/read_matrix.R R/motif_clusters.R R/utils-motif.R R/write_matrix.R R/run_meme.R R/motif_rc.R R/motif_peaks.R R/universalmotif-class.R R/motif_pvalue.R R/create_motif.R R/read_transfac.R R/write_meme.R R/write_transfac.R R/universalmotif.R R/switch_alph.R R/universalmotif-methods.R R/zzz.R R/get_bkg.R R/sample_sites.R R/read_cisbp.R R/create_sequences.R R/trim_motifs.R R/write_jaspar.R R/convert_motifs.R R/motif_finder.R R/shuffle_sequences.R R/compare_motifs.R

src/Makevars.win

src/Makevars

src/get_bkg.cpp

src/trim_motifs.cpp

src/utils-exported.cpp

src/RcppExports.cpp

src/motif_finder.cpp

src/motif_pvalue.cpp

src/shuffle_sequences.h

src/motif_peaks.cpp

src/scan_sequences.cpp

src/utils-internal.h

src/add_multifreq.cpp

src/utils-exported.h

src/compare_motifs.cpp

src/utils-internal.cpp

src/shuffle_sequences.cpp

src/types.h

src/universalmotif-class.cpp

inst/REFERENCES.bib

inst/doc/MotifComparisonAndPvalues.R inst/doc/MotifManipulation.pdf inst/doc/IntroductionToSequenceMotifs.R inst/doc/IntroductionToSequenceMotifs.Rmd inst/doc/MotifManipulation.Rmd inst/doc/IntroductionToSequenceMotifs.pdf inst/doc/MotifManipulation.R inst/doc/MotifComparisonAndPvalues.Rmd inst/doc/Introduction.R inst/doc/SequenceSearches.R inst/doc/Introduction.Rmd inst/doc/SequenceSearches.Rmd inst/doc/Introduction.pdf inst/doc/SequenceSearches.pdf inst/doc/MotifComparisonAndPvalues.pdf

inst/extdata/homer.txt

inst/extdata/hocomoco.txt

inst/extdata/jaspar.txt

inst/extdata/transfac.txt

inst/extdata/sites.txt

inst/extdata/meme_minimal.txt

inst/extdata/universalmotif.txt

inst/extdata/uniprobe_minimal.txt

inst/extdata/dreme.txt

inst/extdata/cisbp.txt

inst/extdata/uniprobe_full.txt

inst/extdata/meme_full.txt

inst/figures/example.png

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/spelling.R tests/testthat/test_add_multifreq.R tests/testthat/test_write_motifs.R tests/testthat/test_motif_tree.R tests/testthat/test_compare_motifs.R tests/testthat/test_get_bkg.R tests/testthat/test_motif_rc.R tests/testthat/test_motif_pvalue.R tests/testthat/test_shuffle_motifs.R tests/testthat/test_universalmotif-methods.R tests/testthat/test_create_sequences.R tests/testthat/test_convert_motifs.R tests/testthat/test_read_motifs.R tests/testthat/test_enrich_motifs.R tests/testthat/test_view_motifs.R tests/testthat/test_convert_type.R tests/testthat/test_sample_sites.R tests/testthat/test_trim_motifs.R tests/testthat/test_motif_peaks.R tests/testthat/test_merge_motifs.R tests/testthat/test_switch_alph.R tests/testthat/test_create_motif.R tests/testthat/test_shuffle_sequences.R tests/testthat/test_utils.R tests/testthat/test_scan_sequences.R tests/testthat/test_filter_motifs.R tests/testthat/test_run_meme.R vignettes/IntroductionToSequenceMotifs.Rmd vignettes/MotifManipulation.Rmd vignettes/MotifComparisonAndPvalues.Rmd vignettes/Introduction.Rmd vignettes/SequenceSearches.Rmd

vignettes/universalmotif.bib

data/JASPAR2018_CORE_DBSCORES.rda

data/examplemotif2.rda

data/ArabidopsisMotif.rda

data/examplemotif.rda

data/ArabidopsisPromoters.rda

man/convert_motifs.Rd man/shuffle_motifs.Rd man/motif_peaks.Rd man/read_transfac.Rd man/filter_motifs.Rd man/read_meme.Rd man/read_homer.Rd man/make_DBscores.Rd man/motif_rc.Rd man/enrich_motifs.Rd man/reexports.Rd man/utils-motif.Rd man/trim_motifs.Rd man/compare_motifs.Rd man/utilities.Rd man/sample_sites.Rd man/get_bkg.Rd man/shuffle_sequences.Rd man/ArabidopsisMotif.Rd man/merge_motifs.Rd man/utils-sequence.Rd man/motif_pvalue.Rd man/ArabidopsisPromoters.Rd man/write_meme.Rd man/read_jaspar.Rd man/run_meme.Rd man/universalmotif-class.Rd man/write_jaspar.Rd man/switch_alph.Rd man/read_matrix.Rd man/write_homer.Rd man/examplemotif.Rd man/read_cisbp.Rd man/convert_type.Rd man/write_transfac.Rd man/read_uniprobe.Rd man/create_sequences.Rd man/examplemotif2.Rd man/view_motifs.Rd man/motif_tree.Rd man/read_motifs.Rd man/scan_sequences.Rd man/universalmotif-pkg.Rd man/add_multifreq.Rd man/write_matrix.Rd man/create_motif.Rd man/JASPAR2018_CORE_DBSCORES.Rd man/write_motifs.Rd

universalmotif documentation built on April 8, 2021, 6 p.m.