Files in snystrom/memes
motif matching, comparison, and de novo discovery using the MEME Suite
.Rbuildignore
.github/.gitignore
.github/workflows/bioc-check.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/ame.R
R/ame_methods.R
R/class_utils.R
R/data.R
R/dreme.R
R/fimo.R
R/generics.R
R/globals.R
R/import_xml.R
R/import_xml_utils.R
R/input_methods.R
R/match_utils.R
R/meme.R
R/memes-package.R
R/motif_utils.R
R/plots.R
R/process_utils.R
R/remove_duplicate_motifs.R
R/sequence_heatmap.R
R/streme.R
R/tomtom.R
R/utils.R
R/utils_internal.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data-raw/example_ame.R
data-raw/example_ame_large.R
data-raw/example_chip_summits.R
data-raw/example_dreme.R
data-raw/example_dreme_by_binding.R
data-raw/example_dreme_tomtom.R
data-raw/example_fimo.R
data-raw/example_peaks.R
data-raw/example_rnaseq_table.R
data-raw/example_tomtom.R
data-raw/flyFactorMotifs.R
data/example_ame.rda
data/example_ame_large.rda
data/example_chip_summits.rda
data/example_dreme.rda
data/example_dreme_by_binding.rda
data/example_dreme_tomtom.rda
data/example_fimo.rda
data/example_peaks.rda
data/example_rnaseq.rda
data/example_tomtom.rda
docs/index.html
inst/CITATION
inst/extdata/ame.tsv
inst/extdata/db/fly_factor_survey.meme
inst/extdata/db/fly_factor_survey_id.meme
inst/extdata/dreme.xml
inst/extdata/example.meme
inst/extdata/fasta_ex/fa1.fa
inst/extdata/fasta_ex/fa2.fa
inst/extdata/fimo.tsv
inst/extdata/flyFactorSurvey_cleaned.meme
inst/extdata/flyFactor_dups.meme
inst/extdata/peaks/peaks.tsv
inst/extdata/sequences.tsv
inst/extdata/streme.xml
inst/extdata/tomtom.xml
inst/extdata/tomtom_bad.xml
man/add_sequence.Rd
man/ame_compare_heatmap_methods.Rd
man/check_meme_install.Rd
man/drop_best_match.Rd
man/example_ame.Rd
man/example_ame_large.Rd
man/example_chip_summits.Rd
man/example_dreme.Rd
man/example_dreme_by_binding.Rd
man/example_dreme_tomtom.Rd
man/example_fimo.Rd
man/example_peaks.Rd
man/example_rnaseq.Rd
man/example_tomtom.Rd
man/figures/README-unnamed-chunk-10-1.png
man/figures/README-unnamed-chunk-11-1.png
man/figures/README-unnamed-chunk-12-1.png
man/figures/README-unnamed-chunk-13-1.png
man/figures/README-unnamed-chunk-13-2.png
man/figures/README-unnamed-chunk-13-3.png
man/figures/README-unnamed-chunk-14-1.png
man/figures/README-unnamed-chunk-14-2.png
man/figures/README-unnamed-chunk-15-1.png
man/figures/README-unnamed-chunk-16-1.png
man/figures/README-unnamed-chunk-17-1.png
man/figures/README-unnamed-chunk-17-2.png
man/figures/README-unnamed-chunk-17-3.png
man/figures/README-unnamed-chunk-17-4.png
man/figures/README-unnamed-chunk-18-1.png
man/figures/README-unnamed-chunk-18-2.png
man/figures/README-unnamed-chunk-18-3.png
man/figures/README-unnamed-chunk-18-4.png
man/figures/README-unnamed-chunk-19-1.png
man/figures/README-unnamed-chunk-20-1.png
man/figures/README-unnamed-chunk-21-1.png
man/figures/README-unnamed-chunk-22-1.png
man/figures/README-unnamed-chunk-25-1.png
man/figures/README-unnamed-chunk-26-1.png
man/figures/README-unnamed-chunk-6-1.png
man/figures/README-unnamed-chunk-7-1.png
man/figures/README-unnamed-chunk-8-1.png
man/force_best_match.Rd
man/get_sequence.Rd
man/has_duplicate_motifs.Rd
man/importAme.Rd
man/importDremeXML.Rd
man/importFimo.Rd
man/importMeme.Rd
man/importStremeXML.Rd
man/importTomTomXML.Rd
man/meme_is_installed.Rd
man/memes-package.Rd
man/nest_tomtom.Rd
man/plot_ame_heatmap.Rd
man/plot_sequence_heatmap.Rd
man/remove_duplicate_motifs.Rd
man/runAme.Rd
man/runDreme.Rd
man/runFimo.Rd
man/runMeme.Rd
man/runStreme.Rd
man/runTomTom.Rd
man/update_best_match.Rd
man/view_tomtom_hits.Rd
man/write_fasta.Rd
tests/testthat.R
tests/testthat/test-ame.R
tests/testthat/test-ame_methods.R
tests/testthat/test-dreme.R
tests/testthat/test-fimo.R
tests/testthat/test-input_methods.R
tests/testthat/test-match_utils.R
tests/testthat/test-meme.R
tests/testthat/test-motif_utils.R
tests/testthat/test-process_error_check.R
tests/testthat/test-remove_duplicate_motifs.R
tests/testthat/test-sequence_heatmap.R
tests/testthat/test-streme.R
tests/testthat/test-tomtom.R
tests/testthat/test-utils.R
tests/testthat/test-xml_import.R
todo.org
vignettes/.gitignore
vignettes/core_ame.Rmd
vignettes/core_dreme.Rmd
vignettes/core_fimo.Rmd
vignettes/core_tomtom.Rmd
vignettes/install_guide.Rmd
vignettes/integrative_analysis.Rmd
vignettes/save_ame.png
vignettes/save_dreme.png
vignettes/save_fimo.png
vignettes/save_tomtom.png
vignettes/tidy_motifs.Rmd
