A B C D E G H L M N P R S T W misc
ChIPseqR-package | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
$,ReadCounts,ANY-method | Class "ReadCounts" |
$<-,ReadCounts,ANY,ANY-method | Class "ReadCounts" |
$<-,ReadCounts-method | Class "ReadCounts" |
alignFeature | Read counts relative to annotated features |
as.data.frame,BindScore-method | Class "BindScore" |
binding | Access slots of S4 classes |
binding,ANY-method | Access slots of S4 classes |
binding,BindScore-method | Class "BindScore" |
binding-methods | Access slots of S4 classes |
BindScore | Class "BindScore" |
BindScore-class | Class "BindScore" |
callBindingSites | Predict protein binding sites from high-throughput sequencing data |
callBindingSites,ANY-method | Predict protein binding sites from high-throughput sequencing data |
callBindingSites,character-method | Predict protein binding sites from high-throughput sequencing data |
callBindingSites,matrix-method | Predict protein binding sites from high-throughput sequencing data |
callBindingSites,ReadCounts-method | Predict protein binding sites from high-throughput sequencing data |
callBindingSites-methods | Predict protein binding sites from high-throughput sequencing data |
ChIPseqR | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
chrLength | Class "ReadCounts" |
chrLength,BindScore-method | Class "BindScore" |
chrLength,ReadCounts-method | Class "ReadCounts" |
chrLength,RLEReadCounts-method | Run-length Encoded Read Counts |
compress | Methods for Function compress in Package 'ChIPseqR' |
compress,BindScore-method | Compress BindScore Objects |
compress,ReadCounts-method | Compress ReadCount Objects |
compress,RLEBindScore-method | Methods for Function compress in Package 'ChIPseqR' |
compress,RLEReadCounts-method | Methods for Function compress in Package 'ChIPseqR' |
compress-BindScore | Compress BindScore Objects |
compress-methods | Methods for Function compress in Package 'ChIPseqR' |
cutoff | Access slots of S4 classes |
cutoff,ANY-method | Access slots of S4 classes |
cutoff,BindScore-method | Class "BindScore" |
cutoff-methods | Access slots of S4 classes |
cutoff<- | Access slots of S4 classes |
cutoff<-,ANY-method | Access slots of S4 classes |
cutoff<-,BindScore-method | Class "BindScore" |
cutoff<--methods | Access slots of S4 classes |
decompress | Extract Read Count and Binding Site Score Representations |
decompress,ANY-method | Methods for Function decompress in Package 'ChIPseqR' |
decompress,Rle-method | Methods for Function decompress in Package 'ChIPseqR' |
decompress,RLEBindScore-method | Extract Read Count and Binding Site Score Representations |
decompress,RleList-method | Methods for Function decompress in Package 'ChIPseqR' |
decompress,RLEReadCounts-method | Extract Read Count and Binding Site Score Representations |
decompress-methods | Methods for Function decompress in Package 'ChIPseqR' |
exportBindSequence | Export sequence of predicted binding sites |
getBindCor | Calculate cross-correlation between read counts |
getBindLen | Estimate length of binding and support region |
getCutoff | Determine significance threshold for binding site scores |
head,BindScore-method | Class "BindScore" |
lapply,BindScore-method | Class "BindScore" |
lapply,ReadCounts-method | Class "ReadCounts" |
length,BindScore-method | Class "BindScore" |
length,ReadCounts-method | Class "ReadCounts" |
length<-,BindScore-method | Class "BindScore" |
length<-,ReadCounts-method | Class "ReadCounts" |
max,BindScore-method | Class "BindScore" |
min,BindScore-method | Class "BindScore" |
names,BindScore-method | Class "BindScore" |
names,ReadCounts-method | Class "ReadCounts" |
names<-,BindScore,ANY-method | Class "BindScore" |
names<-,ReadCounts,ANY-method | Class "ReadCounts" |
nreads | Class "ReadCounts" |
nreads,ReadCounts-method | Class "ReadCounts" |
nreads,RLEReadCounts-method | Run-length Encoded Read Counts |
nullDist | Access slots of S4 classes |
nullDist,ANY-method | Access slots of S4 classes |
nullDist,BindScore-method | Class "BindScore" |
nullDist-methods | Access slots of S4 classes |
nullDist<- | Access slots of S4 classes |
nullDist<-,ANY-method | Access slots of S4 classes |
nullDist<-,BindScore-method | Class "BindScore" |
nullDist<--methods | Access slots of S4 classes |
peaks | Access slots of S4 classes |
peaks,ANY-method | Access slots of S4 classes |
peaks,BindScore-method | Class "BindScore" |
peaks-methods | Access slots of S4 classes |
pickPeak | Identify peaks above a given threshold |
plot,BindScore,missing-method | Diagnostic Plots for Binding Site Scores |
plot,ReadCounts,missing-method | Diagnostic Plots for Read Counts |
plot,RLEReadCounts,missing-method | Diagnostic Plots for Read Counts |
pos2gff | Convert genome coordinates into GFF format |
pvalue | Access slots of S4 classes |
pvalue,ANY-method | Access slots of S4 classes |
pvalue-methods | Access slots of S4 classes |
range,BindScore-method | Class "BindScore" |
ReadCounts | Class "ReadCounts" |
ReadCounts-class | Class "ReadCounts" |
RLEBindScore-class | Run-length Encoded Binding Site Scores |
RLEReadCounts-class | Run-length Encoded Read Counts |
sapply,ReadCounts-method | Class "ReadCounts" |
score | Access slots of S4 classes |
score,BindScore-method | Class "BindScore" |
simpleNucCall | Predict nucleosome positions from high-throughput sequencing data |
startScore | Score potential protein binding sites |
strandPileup | Strand specific read counts |
strandPileup,AlignedRead-method | Strand specific read counts |
strandPileup,data.frame-method | Strand specific read counts |
strandPileup-methods | Strand specific read counts |
support | Access slots of S4 classes |
support,ANY-method | Access slots of S4 classes |
support,BindScore-method | Class "BindScore" |
support-methods | Access slots of S4 classes |
tail,BindScore-method | Class "BindScore" |
windowCounts | Summarize read counts in a sliding window |
[,BindScore,ANY,missing,missing-method | Class "BindScore" |
[,ReadCounts,ANY,missing,missing-method | Class "ReadCounts" |
[<-,ReadCounts,ANY,missing-method | Class "ReadCounts" |
[[,BindScore,ANY,missing-method | Class "BindScore" |
[[,BindScore,ANY,numeric-method | Class "BindScore" |
[[,ReadCounts,ANY,missing-method | Class "ReadCounts" |
[[<-,ReadCounts,ANY,missing-method | Class "ReadCounts" |