cobindR: Finding Co-occuring motifs of transcription factor binding sites

Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cobindR")
AuthorManuela Benary, Stefan Kroeger, Yuehien Lee, Robert Lehmann
Bioconductor views CellBiology ChIPSeq MultipleComparison SequenceMatching
Date of publicationNone
MaintainerManuela Benary <manuela.benary@cms.hu-berlin.de>
LicenseArtistic-2.0
Version1.12.0

View on Bioconductor

Man pages

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.

Functions

bg_binding_sites Man page
bg_binding_sites<- Man page
bg_binding_sites<-,cobindr,data.frame-method Man page
bg_binding_sites,cobindr-method Man page
bg_pairs Man page
bg_pairs<- Man page
bg_pairs<-,cobindr,data.frame-method Man page
bg_pairs,cobindr-method Man page
bg_sequence_origin Man page
bg_sequence_origin<- Man page
bg_sequence_origin<-,configuration,character-method Man page
bg_sequence_origin,configuration-method Man page
bg_sequences Man page
bg_sequences<- Man page
bg_sequences<-,cobindr,list-method Man page
bg_sequences,cobindr-method Man page
bg_sequence_source Man page
bg_sequence_source<- Man page
bg_sequence_source<-,configuration,character-method Man page
bg_sequence_source,configuration-method Man page
bg_sequence_type Man page
bg_sequence_type<- Man page
bg_sequence_type<-,configuration,character-method Man page
bg_sequence_type,configuration-method Man page
binding_sites Man page
binding_sites<- Man page
binding_sites<-,cobindr,data.frame-method Man page
binding_sites,cobindr-method Man page
cobindr Man page
cobindR Man page
cobindr-class Man page
cobindRConfiguration Man page
cobindRConfiguration,character-method Man page
cobindRConfiguration-method Man page
cobindr-package Man page
cobindR-package Man page
comment Man page
comment<- Man page
comment<-,SeqObj,character-method Man page
comment,SeqObj-method Man page
compare.samples Man page
configuration Man page
configuration<- Man page
configuration-class Man page
configuration<-,cobindr,configuration-method Man page
configuration,cobindr-method Man page
cpg.content Man page
cpg.gc.content Man page
determine.cores.option Man page
detrending Man page
detrending,cobindr-method Man page
downstream Man page
downstream<- Man page
downstream,configuration-method Man page
downstream<-,configuration,numeric-method Man page
experiment_description Man page
experiment_description<- Man page
experiment_description<-,cobindr,character-method Man page
experiment_description,cobindr-method Man page
experiment_description<-,configuration,character-method Man page
experiment_description,configuration-method Man page
fdrThreshold Man page
fdrThreshold<- Man page
fdrThreshold,configuration-method Man page
fdrThreshold<-,configuration,numeric-method Man page
find.hits Man page
find.pairs Man page
find.pairs,cobindr-method Man page
find.pairs_intern Man page
gc.content Man page
generate.background Man page
generate.background,cobindr-method Man page
get.bindingsite.ranges Man page
get.bindingsite.ranges,cobindr-method Man page
get.pairs Man page
get.pairs,cobindr-method Man page
get.pairs-method Man page
get.positions Man page
get.significant.pairs Man page
get.significant.pairs,cobindr-method Man page
get.significant.pairs-method Man page
global.permutation Man page
id Man page
id<- Man page
id<-,configuration,character-method Man page
id,configuration-method Man page
initialize,cobindr-method Man page
initialize,configuration-method Man page
initialize,SeqObj-method Man page
input.pfm.similarity Man page
input.pwm Man page
input.pwm,cobindr-method Man page
kl.dist Man page
lcm.vector Man page
local.permutation Man page
location Man page
location<- Man page
location<-,SeqObj,character-method Man page
location,SeqObj-method Man page
make.character Man page
mart Man page
mart<- Man page
mart<-,configuration,character-method Man page
mart,configuration-method Man page
max_distance Man page
max_distance<- Man page
max_distance,configuration-method Man page
max_distance<-,configuration,numeric-method Man page
name Man page
name<- Man page
name<-,cobindr,character-method Man page
name,cobindr-method Man page
name<-,SeqObj,character-method Man page
name,SeqObj-method Man page
normalize.matrix.colSum Man page
pairs Man page
pairs<- Man page
pairs<-,cobindr,data.frame-method Man page
pairs,cobindr-method Man page
pairs<-,configuration,character-method Man page
pairs,configuration-method Man page
pairs_of_interest Man page
pairs_of_interest<- Man page
pairs_of_interest<-,cobindr,factor-method Man page
pairs_of_interest,cobindr-method Man page
parallelize Man page
path Man page
path<- Man page
path<-,configuration,character-method Man page
path,configuration-method Man page
pfm Man page
pfm<- Man page
pfm2pwm Man page
pfm<-,cobindr,list-method Man page
pfm,cobindr-method Man page
pfm_path Man page
pfm_path<- Man page
pfm_path<-,configuration,character-method Man page
pfm_path,configuration-method Man page
pfm.similarity Man page
plot.detrending Man page
plot.detrending,cobindr-method Man page
plot.detrending-method Man page
plot.gc Man page
plot.gc,cobindr-method Man page
plot.gc-method Man page
plot.pairdistance Man page
plot.pairdistance,cobindr-method Man page
plot.pairdistance-method Man page
plot.pairdistribution Man page
plot.pairdistribution,cobindr-method Man page
plot.pairdistribution-method Man page
plot.positionprofile Man page
plot.positionprofile,cobindr-method Man page
plot.positionprofile-method Man page
plot.positions Man page
plot.positions,cobindr-method Man page
plot.positions-method Man page
plot.positions.simple Man page
plot.positions.simple,cobindr-method Man page
plot.positions.simple-method Man page
plot.tfbs.heatmap Man page
plot.tfbs.heatmap,cobindr-method Man page
plot.tfbs.heatmap-method Man page
plot.tfbslogo Man page
plot.tfbslogo,cobindr-method Man page
plot.tfbslogo-method Man page
plot.tfbs.venndiagram Man page
plot.tfbs.venndiagram,cobindr-method Man page
plot.tfbs.venndiagram-method Man page
predicted2pwm Man page
predicted2pwm,cobindr-method Man page
predicted2pwm-method Man page
pseudocount Man page
pseudocount<- Man page
pseudocount<-,configuration,character-method Man page
pseudocount,configuration-method Man page
pValue Man page
pValue<- Man page
pValue,configuration-method Man page
pValue<-,configuration,numeric-method Man page
query.motifDb Man page
read.background.fasta Man page
read.background.fasta,configuration-method Man page
read.pfm Man page
read.pfm,configuration-method Man page
read.sequences Man page
read.sequences,configuration-method Man page
read.transfac.pfm Man page
removeSpecialCharacters Man page
rtfbs Man page
rtfbs,cobindr-method Man page
rtfbs.intern Man page
rtfbs.intern,SeqObj-method Man page
rtfbs-method Man page
search.gadem Man page
search.gadem,cobindr-method Man page
search.gadem-method Man page
search.pwm Man page
search.pwm,cobindr-method Man page
search.pwm-method Man page
seqObj Man page
SeqObj-class Man page
seqObj,DNAString,character,character,character,character,charact Man page
seqObj-method Man page
sequence Man page
sequence<- Man page
sequence_origin Man page
sequence_origin<- Man page
sequence_origin<-,configuration,character-method Man page
sequence_origin,configuration-method Man page
sequences Man page
sequences<- Man page
sequences<-,cobindr,list-method Man page
sequences,cobindr-method Man page
sequence<-,SeqObj,DNAString-method Man page
sequence,SeqObj-method Man page
sequence_source Man page
sequence_source<- Man page
sequence_source<-,configuration,character-method Man page
sequence_source,configuration-method Man page
sequence_type Man page
sequence_type<- Man page
sequence_type<-,configuration,character-method Man page
sequence_type,configuration-method Man page
species Man page
species<- Man page
species<-,configuration-method Man page
species,configuration-method Man page
species<-,SeqObj-method Man page
species,SeqObj-method Man page
testCpG Man page
testCpG,cobindr-method Man page
testCpG-method Man page
threshold Man page
threshold<- Man page
threshold,configuration-method Man page
threshold<-,configuration,numeric-method Man page
uid Man page
uid<- Man page
uid<-,cobindr,character-method Man page
uid,cobindr-method Man page
uid<-,SeqObj,character-method Man page
uid,SeqObj-method Man page
uniqueFilename Man page
upstream Man page
upstream<- Man page
upstream,configuration-method Man page
upstream<-,configuration,numeric-method Man page
wind.cpg.content Man page
wind.cpg.gc.content Man page
wind.gc.content Man page
write.bindingsites Man page
write.bindingsites,cobindr-method Man page
write.bindingsites-method Man page
write.bindingsites.table Man page
write.bindingsites.table,cobindr-method Man page
write.bindingsites.table-method Man page
write,cobindr,character-method Man page
write,configuration,character-method Man page
writeDetrending_intern Man page
write.fasta,SeqObj-method Man page
write.pairs Man page
write.pairs,cobindr-method Man page
write.pairs-method Man page
write.sequences Man page
write.sequences,cobindr-method Man page
write.sequences-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/accessMethods.R R/backgrounds.R R/detrending.R R/findPairs.R R/initialize-methods.R R/parallelize.R R/plot-methods.R R/pwm_io.R R/rtfbs.R R/sequence_io.R R/tfbsSearch.R R/write-methods.R
build
build/vignette.rds
inst
inst/doc
inst/doc/cobindR.R
inst/doc/cobindR.Rnw
inst/doc/cobindR.pdf
inst/extdata
inst/extdata/config_default.yml
inst/extdata/example.fasta
inst/extdata/pfms
inst/extdata/pfms/myod.tfpfm
inst/extdata/pfms/soxoctklf.tfpfm
inst/extdata/sox_oct_example_vignette_seqs.fasta
inst/extdata/ucsc_example_ItemRGBDemo.bed
inst/unitTests
inst/unitTests/runit-cobindR.R inst/unitTests/runit-configuration.R
man
man/SeqObj-class.Rd man/bg_binding_sites.Rd man/bg_pairs.Rd man/bg_sequence_origin.Rd man/bg_sequence_source.Rd man/bg_sequence_type.Rd man/bg_sequences.Rd man/binding_sites.Rd man/cobindRConfiguration.Rd man/cobindr-class.Rd man/cobindr-internal.Rd man/cobindr-package.Rd man/comment.Rd man/configuration-class.Rd man/configuration.Rd man/downstream.Rd man/experiment_description.Rd man/fdrThreshold.Rd man/find.pairs.Rd man/get.bindingsite.ranges.Rd man/get.pairs.Rd man/get.significant.pairs.Rd man/id.Rd man/location.Rd man/mart.Rd man/max_distance.Rd man/name.Rd man/pValue.Rd man/pairs.Rd man/pairs_of_interest.Rd man/path.Rd man/pfm.Rd man/pfm_path.Rd man/plot.detrending.Rd man/plot.gc.Rd man/plot.pairdistance.Rd man/plot.pairdistribution.Rd man/plot.positionprofile.Rd man/plot.positions.Rd man/plot.positions.simple.Rd man/plot.tfbs.heatmap.Rd man/plot.tfbs.venndiagram.Rd man/plot.tfbslogo.Rd man/predicted2pwm.Rd man/pseudocount.Rd man/rtfbs.Rd man/search.gadem.Rd man/search.pwm.Rd man/seqObj.Rd man/sequence.Rd man/sequence_origin.Rd man/sequence_source.Rd man/sequence_type.Rd man/sequences.Rd man/species.Rd man/testCpG.Rd man/threshold.Rd man/uid.Rd man/upstream.Rd man/write.bindingsites.Rd man/write.bindingsites.table.Rd man/write.pairs.Rd man/write.sequences.Rd
tests
tests/runTests.R
vignettes
vignettes/cobindR.Rnw
vignettes/img
vignettes/img/cobindR-plot_detrending.pdf
vignettes/img/cobindR-plot_gc_test.pdf
vignettes/img/cobindR-plot_heatmap.pdf
vignettes/img/cobindR-plot_pairdistance.pdf
vignettes/img/cobindR-plot_pairdistribution.pdf
vignettes/img/cobindR-plot_positions_profile.pdf
vignettes/img/cobindR-plot_positions_simple.pdf
vignettes/img/cobindR-plot_predicted_logos.pdf
vignettes/img/cobindR-plot_venn.pdf

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