Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes
|Author||Manuela Benary, Stefan Kroeger, Yuehien Lee, Robert Lehmann|
|Date of publication||None|
|Maintainer||Manuela Benary <email@example.com>|
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_sequences: list of background sequence
bg_sequence_source: background sequence source note
bg_sequence_type: background sequence type note
binding_sites: motif hits on the foreground sequences
cobindr-class: Class '"cobindr"'
cobindRConfiguration: cobindR configuration object constructor
cobindr-internal: Internal cobindr Functions
cobindr-package: An R package for analyzing co-occurring transcription factor...
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...
get.bindingsite.ranges: convenience function to convert predicted binding sites to...
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
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...
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...
plot.positionprofile: function to plot a profile over the total number of predicted...
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...
plot.tfbslogo: function to plot sequence logos based on hits of tools
plot.tfbs.venndiagram: function visualize the overlaps of PWM hits over the...
predicted2pwm: function to convert predicted TFBS hits into a PWM
pseudocount: pseudocount of cobindR configuration object
pValue: pValue threshold used for motif hit finding
rtfbs: function performs TFBS prediction using the package rtfbs
search.gadem: function performs TFBS prediction denovo or based on transfac...
search.pwm: function to predict transcription factor binding sites using...
seqObj: cobindR SeqObj object constructor
SeqObj-class: Class '"SeqObj"'
sequence: returns sequence of cobindR SeqObj object
sequence_origin: returns sequence_origin of cobindR configuration object
sequences: sequences of cobindr object
sequence_source: returns sequence_source of cobindR configuration object
sequence_type: sequence type of cobindR configuration object
species: species of cobindR configuration or SeqObj
testCpG: function to cluster sequences based on their CpG and GC...
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.