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. |