API for Bioconductor-mirror/cobindR
Finding Co-occuring motifs of transcription factor binding sites

Global functions
SeqObj-class Man page
bg_binding_sites Man page
bg_binding_sites,cobindr-method Man page
bg_binding_sites<- Man page
bg_binding_sites<-,cobindr,data.frame-method Man page
bg_pairs Man page
bg_pairs,cobindr-method Man page
bg_pairs<- Man page
bg_pairs<-,cobindr,data.frame-method Man page
bg_sequence_origin Man page
bg_sequence_origin,configuration-method Man page
bg_sequence_origin<- Man page
bg_sequence_origin<-,configuration,character-method Man page
bg_sequence_source Man page
bg_sequence_source,configuration-method Man page
bg_sequence_source<- Man page
bg_sequence_source<-,configuration,character-method Man page
bg_sequence_type Man page
bg_sequence_type,configuration-method Man page
bg_sequence_type<- Man page
bg_sequence_type<-,configuration,character-method Man page
bg_sequences Man page
bg_sequences,cobindr-method Man page
bg_sequences<- Man page
bg_sequences<-,cobindr,list-method Man page
binding_sites Man page
binding_sites,cobindr-method Man page
binding_sites<- Man page
binding_sites<-,cobindr,data.frame-method Man page
cobindR Man page
cobindR-package Man page
cobindRConfiguration Man page Source code
cobindRConfiguration,character-method Man page
cobindRConfiguration-method Man page
cobindr Man page Source code
cobindr-class Man page
cobindr-package Man page
comment Man page
comment,SeqObj-method Man page
comment<- Man page
comment<-,SeqObj,character-method Man page
compare.samples Man page Source code
configuration Man page
configuration,cobindr-method Man page
configuration-class Man page
configuration<- Man page
configuration<-,cobindr,configuration-method Man page
cpg.content Man page Source code
cpg.gc.content Man page Source code
determine.cores.option Man page Source code
detrending Man page
detrending,cobindr-method Man page
downstream Man page
downstream,configuration-method Man page
downstream<- Man page
downstream<-,configuration,numeric-method Man page
experiment_description Man page
experiment_description,cobindr-method Man page
experiment_description,configuration-method Man page
experiment_description<- Man page
experiment_description<-,cobindr,character-method Man page
experiment_description<-,configuration,character-method Man page
fdrThreshold Man page
fdrThreshold,configuration-method Man page
fdrThreshold<- Man page
fdrThreshold<-,configuration,numeric-method Man page
find.hits Man page Source code
find.pairs Man page
find.pairs,cobindr-method Man page
find.pairs_intern Man page Source code
gc.content Man page Source code
generate.background Man page
generate.background,cobindr-method Man page
get.bindingsite.ranges Man page
get.bindingsite.ranges,cobindr-method Man page
get.detrending_intern Source code
get.pairs Man page
get.pairs,cobindr-method Man page
get.pairs-method Man page
get.positions Man page Source code
get.significant.pairs Man page
get.significant.pairs,cobindr-method Man page
get.significant.pairs-method Man page
global.permutation Man page Source code
id Man page
id,configuration-method Man page
id<- Man page
id<-,configuration,character-method Man page
initialize,SeqObj-method Man page
initialize,cobindr-method Man page
initialize,configuration-method Man page
input.pfm.similarity Man page Source code
input.pwm Man page
input.pwm,cobindr-method Man page
kl.dist Man page Source code
lcm.vector Man page Source code
local.permutation Man page Source code
location Man page
location,SeqObj-method Man page
location<- Man page
location<-,SeqObj,character-method Man page
make.character Man page Source code
mart Man page
mart,configuration-method Man page
mart<- Man page
mart<-,configuration,character-method Man page
max_distance Man page
max_distance,configuration-method Man page
max_distance<- Man page
max_distance<-,configuration,numeric-method Man page
name Man page
name,SeqObj-method Man page
name,cobindr-method Man page
name<- Man page
name<-,SeqObj,character-method Man page
name<-,cobindr,character-method Man page
normalize.matrix.colSum Man page Source code
pValue Man page
pValue,configuration-method Man page
pValue<- Man page
pValue<-,configuration,numeric-method Man page
pairs Man page
pairs,cobindr-method Man page
pairs,configuration-method Man page
pairs<- Man page
pairs<-,cobindr,data.frame-method Man page
pairs<-,configuration,character-method Man page
pairs_of_interest Man page
pairs_of_interest,cobindr-method Man page
pairs_of_interest<- Man page
pairs_of_interest<-,cobindr,factor-method Man page
parallelize Man page Source code
path Man page
path,configuration-method Man page
path<- Man page
path<-,configuration,character-method Man page
pfm Man page
pfm,cobindr-method Man page
pfm.similarity Man page Source code
pfm2pwm Man page Source code
pfm<- Man page
pfm<-,cobindr,list-method Man page
pfm_path Man page
pfm_path,configuration-method Man page
pfm_path<- Man page
pfm_path<-,configuration,character-method 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.tfbs.venndiagram Man page
plot.tfbs.venndiagram,cobindr-method Man page
plot.tfbs.venndiagram-method Man page
plot.tfbslogo Man page
plot.tfbslogo,cobindr-method Man page
plot.tfbslogo-method Man page
predicted2pwm Man page
predicted2pwm,cobindr-method Man page
predicted2pwm-method Man page
pseudocount Man page
pseudocount,configuration-method Man page
pseudocount<- Man page
pseudocount<-,configuration,character-method Man page
query.motifDb Man page Man page Source code
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 Source code
removeSpecialCharacters Man page Source code
rtfbs Man page
rtfbs,cobindr-method Man page
rtfbs-method Man page
rtfbs.intern Man page
rtfbs.intern,SeqObj-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 Source code
seqObj,DNAString,character,character,character,character,charact Man page
seqObj-method Man page
sequence Man page
sequence,SeqObj-method Man page
sequence<- Man page
sequence<-,SeqObj,DNAString-method Man page
sequence_origin Man page
sequence_origin,configuration-method Man page
sequence_origin<- Man page
sequence_origin<-,configuration,character-method Man page
sequence_source Man page
sequence_source,configuration-method Man page
sequence_source<- Man page
sequence_source<-,configuration,character-method Man page
sequence_type Man page
sequence_type,configuration-method Man page
sequence_type<- Man page
sequence_type<-,configuration,character-method Man page
sequences Man page
sequences,cobindr-method Man page
sequences<- Man page
sequences<-,cobindr,list-method Man page
species Man page
species,SeqObj-method Man page
species,configuration-method Man page
species<- Man page
species<-,SeqObj-method Man page
species<-,configuration-method Man page
testCpG Man page
testCpG,cobindr-method Man page
testCpG-method Man page
threshold Man page
threshold,configuration-method Man page
threshold<- Man page
threshold<-,configuration,numeric-method Man page
uid Man page
uid,SeqObj-method Man page
uid,cobindr-method Man page
uid<- Man page
uid<-,SeqObj,character-method Man page
uid<-,cobindr,character-method Man page
uniqueFilename Man page Source code
upstream Man page
upstream,configuration-method Man page
upstream<- Man page
upstream<-,configuration,numeric-method Man page
wind.cpg.content Man page Source code
wind.cpg.gc.content Man page
wind.gc.content Man page Source code
write,cobindr,character-method Man page
write,configuration,character-method 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.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
writeDetrending_intern Man page
Bioconductor-mirror/cobindR documentation built on June 1, 2017, 6:37 a.m.