Files in cobindR
Finding Co-occuring motifs of transcription factor binding sites
NEWS
NAMESPACE
DESCRIPTION
build/vignette.rds
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/cobindR.Rnw
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.Rnw
inst/doc/cobindR.pdf
inst/doc/cobindR.R
inst/extdata/example.fasta
inst/extdata/config_default.yml
inst/extdata/ucsc_example_ItemRGBDemo.bed
inst/extdata/sox_oct_example_vignette_seqs.fasta
inst/extdata/pfms/soxoctklf.tfpfm
inst/extdata/pfms/myod.tfpfm
inst/unitTests/runit-cobindR.R
inst/unitTests/runit-configuration.R
