Files in cobindR

Finding Co-occuring motifs of transcription factor binding sites

R/accessMethods.R R/parallelize.R R/AllGenerics.R R/sequence_io.R R/detrending.R R/backgrounds.R R/initialize-methods.R R/findPairs.R R/plot-methods.R R/AllClasses.R R/pwm_io.R R/write-methods.R R/tfbsSearch.R R/rtfbs.R vignettes/img/cobindR-plot_venn.pdf vignettes/img/cobindR-plot_predicted_logos.pdf vignettes/img/cobindR-plot_heatmap.pdf vignettes/img/cobindR-plot_detrending.pdf vignettes/img/cobindR-plot_pairdistribution.pdf vignettes/img/cobindR-plot_positions_profile.pdf vignettes/img/cobindR-plot_pairdistance.pdf vignettes/img/cobindR-plot_positions_simple.pdf vignettes/img/cobindR-plot_gc_test.pdf man/plot.pairdistance.Rd man/search.pwm.Rd man/sequences.Rd man/location.Rd man/write.bindingsites.Rd man/predicted2pwm.Rd man/pfm_path.Rd man/testCpG.Rd man/sequence_source.Rd man/plot.tfbslogo.Rd man/pairs.Rd man/write.sequences.Rd man/cobindr-class.Rd man/bg_sequence_source.Rd man/find.pairs.Rd man/plot.detrending.Rd man/comment.Rd man/pairs_of_interest.Rd man/bg_sequences.Rd man/bg_sequence_type.Rd man/upstream.Rd man/get.pairs.Rd man/id.Rd man/write.bindingsites.table.Rd man/configuration-class.Rd man/threshold.Rd man/plot.tfbs.venndiagram.Rd man/seqObj.Rd man/cobindr-package.Rd man/get.bindingsite.ranges.Rd man/species.Rd man/plot.tfbs.heatmap.Rd man/plot.positions.simple.Rd man/pseudocount.Rd man/binding_sites.Rd man/downstream.Rd man/experiment_description.Rd man/sequence.Rd man/plot.positions.Rd man/configuration.Rd man/pfm.Rd man/bg_binding_sites.Rd man/pValue.Rd man/path.Rd man/SeqObj-class.Rd man/cobindr-internal.Rd man/cobindRConfiguration.Rd man/mart.Rd man/max_distance.Rd man/rtfbs.Rd man/plot.pairdistribution.Rd man/get.significant.pairs.Rd man/plot.gc.Rd man/write.pairs.Rd man/sequence_origin.Rd man/search.gadem.Rd man/uid.Rd man/sequence_type.Rd man/bg_pairs.Rd man/name.Rd man/fdrThreshold.Rd man/plot.positionprofile.Rd man/bg_sequence_origin.Rd tests/runTests.R inst/doc/cobindR.pdf inst/doc/cobindR.R inst/unitTests/runit-cobindR.R inst/unitTests/runit-configuration.R