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

Author
Manuela Benary, Stefan Kroeger, Yuehien Lee, Robert Lehmann
Date of publication
None
Maintainer
Manuela Benary <manuela.benary@cms.hu-berlin.de>
License
Artistic-2.0
Version
1.12.0

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.

Files in this package

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