![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
B C D E F G I L M N P R S T U W
| cobindR-package | An R package for analyzing co-occurring transcription factor binding sites |
| cobindr-package | An R package for analyzing co-occurring transcription factor binding sites |
| bg_binding_sites | motif hits in the background sequences |
| bg_binding_sites-method | motif hits in the background sequences |
| bg_binding_sites<- | motif hits in the background sequences |
| bg_binding_sites<--method | motif hits in the background sequences |
| bg_pairs | motif hit pairs in the background sequences |
| bg_pairs-method | motif hit pairs in the background sequences |
| bg_pairs<- | motif hit pairs in the background sequences |
| bg_pairs<--method | motif hit pairs in the background sequences |
| bg_sequences | list of background sequence |
| bg_sequences-method | list of background sequence |
| bg_sequences<- | list of background sequence |
| bg_sequences<--method | list of background sequence |
| bg_sequence_origin | background sequence origin note |
| bg_sequence_origin-method | background sequence origin note |
| bg_sequence_origin<- | background sequence origin note |
| bg_sequence_origin<--method | background sequence origin note |
| bg_sequence_source | background sequence source note |
| bg_sequence_source-method | background sequence source note |
| bg_sequence_source<- | background sequence source note |
| bg_sequence_source<--method | background sequence source note |
| bg_sequence_type | background sequence type note |
| bg_sequence_type-method | background sequence type note |
| bg_sequence_type<- | background sequence type note |
| bg_sequence_type<--method | background sequence type note |
| binding_sites | motif hits on the foreground sequences |
| binding_sites-method | motif hits on the foreground sequences |
| binding_sites<- | motif hits on the foreground sequences |
| binding_sites<--method | motif hits on the foreground sequences |
| cobindR | An R package for analyzing co-occurring transcription factor binding sites |
| cobindr | An R package for analyzing co-occurring transcription factor binding sites |
| cobindr-class | Class '"cobindr"' |
| cobindRConfiguration | cobindR configuration object constructor |
| cobindRConfiguration-method | cobindR configuration object constructor |
| comment | comment of cobindR SeqObj object |
| comment-method | comment of cobindR SeqObj object |
| comment<- | comment of cobindR SeqObj object |
| comment<--method | comment of cobindR SeqObj object |
| configuration | configuration of cobindr object |
| configuration-class | Class '"configuration"' |
| configuration-method | configuration of cobindr object |
| configuration<- | configuration of cobindr object |
| configuration<--method | configuration of cobindr object |
| detrending-method | Class '"cobindr"' |
| downstream | downstream range [bp] used in experiment |
| downstream-method | downstream range [bp] used in experiment |
| downstream<- | downstream range [bp] used in experiment |
| downstream<--method | downstream range [bp] used in experiment |
| experiment_description | description of cobindR or configuration object |
| experiment_description-method | description of cobindR or configuration object |
| experiment_description<- | description of cobindR or configuration object |
| experiment_description<--method | description of cobindR or configuration object |
| fdrThreshold | fdrThreshold of cobindR configuration object |
| fdrThreshold-method | fdrThreshold of cobindR configuration object |
| fdrThreshold<- | fdrThreshold of cobindR configuration object |
| fdrThreshold<--method | fdrThreshold of cobindR configuration object |
| find.pairs | function to find pairs of binding sites for every sequence in a given object of class "cobindr" |
| find.pairs-method | Class '"cobindr"' |
| generate.background-method | Class '"cobindr"' |
| get.bindingsite.ranges | convenience function to convert predicted binding sites to GRanges object. |
| get.bindingsite.ranges-method | Class '"cobindr"' |
| get.pairs | function to get output of findPairs |
| get.pairs-method | function to get output of findPairs |
| get.significant.pairs | function to returns the results of detrending as a data.frame |
| get.significant.pairs-method | function to returns the results of detrending as a data.frame |
| id | id of cobindR configuration object |
| id-method | id of cobindR configuration object |
| id<- | id of cobindR configuration object |
| id<--method | id of cobindR configuration object |
| initialize-method | Class '"SeqObj"' |
| initialize-method | Class '"cobindr"' |
| initialize-method | Class '"configuration"' |
| input.pwm-method | Class '"cobindr"' |
| location | location of cobindR SeqObj object |
| location-method | location of cobindR SeqObj object |
| location<- | location of cobindR SeqObj object |
| location<--method | location of cobindR SeqObj object |
| mart | biomart of cobindR configuration object |
| mart-method | biomart of cobindR configuration object |
| mart<- | biomart of cobindR configuration object |
| mart<--method | biomart of cobindR configuration object |
| max_distance | max_distance of cobindR configuration object |
| max_distance-method | max_distance of cobindR configuration object |
| max_distance<- | max_distance of cobindR configuration object |
| max_distance<--method | max_distance of cobindR configuration object |
| name | name of cobindR SeqObj object |
| name-method | name of cobindR SeqObj object |
| name<- | name of cobindR SeqObj object |
| name<--method | name of cobindR SeqObj object |
| pairs | motif hit pairs in the foreground sequences |
| pairs-method | motif hit pairs in the foreground sequences |
| pairs<- | motif hit pairs in the foreground sequences |
| pairs<--method | motif hit pairs in the foreground sequences |
| pairs_of_interest | pairs_of_interest of cobindr object |
| pairs_of_interest-method | pairs_of_interest of cobindr object |
| pairs_of_interest<- | pairs_of_interest of cobindr object |
| pairs_of_interest<--method | pairs_of_interest of cobindr object |
| path | path of cobindR configuration object |
| path-method | path of cobindR configuration object |
| path<- | path of cobindR configuration object |
| path<--method | path of cobindR configuration object |
| pfm | pfm list used in experiment |
| pfm-method | pfm list used in experiment |
| pfm<- | pfm list used in experiment |
| pfm<--method | pfm list used in experiment |
| pfm_path | path to pfms to be used |
| pfm_path-method | path to pfms to be used |
| pfm_path<- | path to pfms to be used |
| pfm_path<--method | path to pfms to be used |
| plot.detrending | function to plot distances between a pair of PWMs |
| plot.detrending-method | function to plot distances between a pair of PWMs |
| plot.gc | function to visualize GC content or CpG content of input sequences |
| plot.gc-method | 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.pairdistance-method | 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.pairdistribution-method | 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.positionprofile-method | 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-method | 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.positions.simple-method | 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.heatmap-method | 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.tfbs.venndiagram-method | function visualize the overlaps of PWM hits over the sequences. |
| plot.tfbslogo | function to plot sequence logos based on hits of tools |
| plot.tfbslogo-method | function to plot sequence logos based on hits of tools |
| predicted2pwm | function to convert predicted TFBS hits into a PWM |
| predicted2pwm-method | function to convert predicted TFBS hits into a PWM |
| pseudocount | pseudocount of cobindR configuration object |
| pseudocount-method | pseudocount of cobindR configuration object |
| pseudocount<- | pseudocount of cobindR configuration object |
| pseudocount<--method | pseudocount of cobindR configuration object |
| pValue | pValue threshold used for motif hit finding |
| pValue-method | pValue threshold used for motif hit finding |
| pValue<- | pValue threshold used for motif hit finding |
| pValue<--method | pValue threshold used for motif hit finding |
| read.background.fasta-method | Class '"configuration"' |
| read.pfm-method | Class '"configuration"' |
| read.sequences-method | Class '"configuration"' |
| rtfbs | function performs TFBS prediction using the package rtfbs |
| rtfbs-method | function performs TFBS prediction using the package rtfbs |
| rtfbs.intern-method | Class '"SeqObj"' |
| search.gadem | function performs TFBS prediction denovo or based on transfac / jaspar matrices pwms using rGADEM. |
| search.gadem-method | 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 |
| search.pwm-method | function to predict transcription factor binding sites using the method matchPWM from package Biostrings |
| seqObj | cobindR SeqObj object constructor |
| SeqObj-class | Class '"SeqObj"' |
| seqObj-method | cobindR SeqObj object constructor |
| sequence | returns sequence of cobindR SeqObj object |
| sequence-method | returns sequence of cobindR SeqObj object |
| sequence<- | returns sequence of cobindR SeqObj object |
| sequence<--method | returns sequence of cobindR SeqObj object |
| sequences | sequences of cobindr object |
| sequences-method | sequences of cobindr object |
| sequences<- | sequences of cobindr object |
| sequences<--method | sequences of cobindr object |
| sequence_origin | returns sequence_origin of cobindR configuration object |
| sequence_origin-method | returns sequence_origin of cobindR configuration object |
| sequence_origin<- | returns sequence_origin of cobindR configuration object |
| sequence_origin<--method | returns sequence_origin of cobindR configuration object |
| sequence_source | returns sequence_source of cobindR configuration object |
| sequence_source-method | returns sequence_source of cobindR configuration object |
| sequence_source<- | returns sequence_source of cobindR configuration object |
| sequence_source<--method | returns sequence_source of cobindR configuration object |
| sequence_type | sequence type of cobindR configuration object |
| sequence_type-method | sequence type of cobindR configuration object |
| sequence_type<- | sequence type of cobindR configuration object |
| sequence_type<--method | sequence type of cobindR configuration object |
| species | species of cobindR configuration or SeqObj |
| species-method | species of cobindR configuration or SeqObj |
| species<- | species of cobindR configuration or SeqObj |
| species<--method | species of cobindR configuration or SeqObj |
| testCpG | function to cluster sequences based on their CpG and GC content |
| testCpG-method | function to cluster sequences based on their CpG and GC content |
| threshold | threshold used in motif hit finding |
| threshold-method | threshold used in motif hit finding |
| threshold<- | threshold used in motif hit finding |
| threshold<--method | threshold used in motif hit finding |
| uid | uid of cobindR SeqObj object |
| uid-method | uid of cobindR SeqObj object |
| uid<- | uid of cobindR SeqObj object |
| uid<--method | uid of cobindR SeqObj object |
| upstream | upstream range [bp] used in experiment |
| upstream-method | upstream range [bp] used in experiment |
| upstream<- | upstream range [bp] used in experiment |
| upstream<--method | upstream range [bp] used in experiment |
| write-method | Class '"cobindr"' |
| write-method | Class '"configuration"' |
| write.bindingsites | writes predicted binding sites as a BED file. |
| write.bindingsites-method | writes predicted binding sites as a BED file. |
| write.bindingsites.table | function to write predicted TFBS into a tab-separated file. |
| write.bindingsites.table-method | function to write predicted TFBS into a tab-separated file. |
| write.fasta-method | Class '"SeqObj"' |
| write.pairs | function to write output of findPairs into file |
| write.pairs-method | function to write output of findPairs into file |
| write.sequences | writes the sequences of a cobindr-object into a fasta file. |
| write.sequences-method | writes the sequences of a cobindr-object into a fasta file. |