SeqObj-class            Class '"SeqObj"'
bg_binding_sites        motif hits in the background sequences
bg_pairs                motif hit pairs in the background sequences
bg_sequence_origin      background sequence origin note
bg_sequence_source      background sequence source note
bg_sequence_type        background sequence type note
bg_sequences            list of background sequence
binding_sites           motif hits on the foreground sequences
cobindR-package         An R package for analyzing co-occurring
                        transcription factor binding sites
cobindRConfiguration    cobindR configuration object constructor
cobindr-class           Class '"cobindr"'
comment                 comment of cobindR SeqObj object
configuration           configuration of cobindr object
configuration-class     Class '"configuration"'
downstream              downstream range [bp] used in experiment
experiment_description
                        description of cobindR or configuration object
fdrThreshold            fdrThreshold of cobindR configuration object
find.pairs              function to find pairs of binding sites for
                        every sequence in a given object of class
                        "cobindr"
get.bindingsite.ranges
                        convenience function to convert predicted
                        binding sites to GRanges object.
get.pairs               function to get output of findPairs
get.significant.pairs   function to returns the results of detrending
                        as a data.frame
id                      id of cobindR configuration object
location                location of cobindR SeqObj object
mart                    biomart of cobindR configuration object
max_distance            max_distance of cobindR configuration object
name                    name of cobindR SeqObj object
pValue                  pValue threshold used for motif hit finding
pairs                   motif hit pairs in the foreground sequences
pairs_of_interest       pairs_of_interest of cobindr object
path                    path of cobindR configuration object
pfm                     pfm list used in experiment
pfm_path                path to pfms to be used
plot.detrending         function to plot distances between a pair of
                        PWMs
plot.gc                 function to visualize GC content or CpG content
                        of input sequences
plot.pairdistance       function to plot the distance of the pairs in
                        the sequences
plot.pairdistribution   function to plot the distribution of the number
                        of pairs in the sequences
plot.positionprofile    function to plot a profile over the total
                        number of predicted transcription factor
                        binding sites for each PWM.
plot.positions          function to plot hits for each PWM on the
                        individual sequence
plot.positions.simple   function to plot hits for each PWM on the
                        individual sequence
plot.tfbs.heatmap       function to do plot a heatmap of overlaps
                        between all specified PWMs
plot.tfbs.venndiagram   function visualize the overlaps of PWM hits
                        over the sequences.
plot.tfbslogo           function to plot sequence logos based on hits
                        of tools
predicted2pwm           function to convert predicted TFBS hits into a
                        PWM
pseudocount             pseudocount of cobindR configuration object
rtfbs                   function performs TFBS prediction using the
                        package rtfbs
search.gadem            function performs TFBS prediction denovo or
                        based on transfac / jaspar matrices pwms using
                        rGADEM.
search.pwm              function to predict transcription factor
                        binding sites using the method matchPWM from
                        package Biostrings
seqObj                  cobindR SeqObj object constructor
sequence                returns sequence of cobindR SeqObj object
sequence_origin         returns sequence_origin of cobindR
                        configuration object
sequence_source         returns sequence_source of cobindR
                        configuration object
sequence_type           sequence type of cobindR configuration object
sequences               sequences of cobindr object
species                 species of cobindR configuration or SeqObj
testCpG                 function to cluster sequences based on their
                        CpG and GC content
threshold               threshold used in motif hit finding
uid                     uid of cobindR SeqObj object
upstream                upstream range [bp] used in experiment
write.bindingsites      writes predicted binding sites as a BED file.
write.bindingsites.table
                        function to write predicted TFBS into a
                        tab-separated file.
write.pairs             function to write output of findPairs into file
write.sequences         writes the sequences of a cobindr-object into a
                        fasta file.
