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 |
alignFeature | Read counts relative to annotated features |
as.data.frame-method | Class "BindScore" |
binding | Access slots of S4 classes |
binding-method | Class "BindScore" |
binding-method | Access slots of S4 classes |
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-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-method | Class "BindScore" |
chrLength-method | Run-length Encoded Read Counts |
chrLength-method | Class "ReadCounts" |
compress | Methods for Function compress in Package 'ChIPseqR' |
compress-BindScore | Compress BindScore Objects |
compress-method | Compress BindScore Objects |
compress-method | Compress ReadCount Objects |
compress-method | Methods for Function compress in Package 'ChIPseqR' |
compress-methods | Methods for Function compress in Package 'ChIPseqR' |
cutoff | Access slots of S4 classes |
cutoff-method | Class "BindScore" |
cutoff-method | Access slots of S4 classes |
cutoff-methods | Access slots of S4 classes |
cutoff<- | Access slots of S4 classes |
cutoff<--method | Class "BindScore" |
cutoff<--method | Access slots of S4 classes |
cutoff<--methods | Access slots of S4 classes |
decompress | Extract Read Count and Binding Site Score Representations |
decompress-method | Methods for Function decompress in Package 'ChIPseqR' |
decompress-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-method | Class "BindScore" |
lapply-method | Class "BindScore" |
lapply-method | Class "ReadCounts" |
length-method | Class "BindScore" |
length-method | Class "ReadCounts" |
length<--method | Class "BindScore" |
length<--method | Class "ReadCounts" |
max-method | Class "BindScore" |
min-method | Class "BindScore" |
names-method | Class "BindScore" |
names-method | Class "ReadCounts" |
names<--method | Class "BindScore" |
names<--method | Class "ReadCounts" |
nreads | Class "ReadCounts" |
nreads-method | Run-length Encoded Read Counts |
nreads-method | Class "ReadCounts" |
nullDist | Access slots of S4 classes |
nullDist-method | Class "BindScore" |
nullDist-method | Access slots of S4 classes |
nullDist-methods | Access slots of S4 classes |
nullDist<- | Access slots of S4 classes |
nullDist<--method | Class "BindScore" |
nullDist<--method | Access slots of S4 classes |
nullDist<--methods | Access slots of S4 classes |
peaks | Access slots of S4 classes |
peaks-method | Class "BindScore" |
peaks-method | Access slots of S4 classes |
peaks-methods | Access slots of S4 classes |
pickPeak | Identify peaks above a given threshold |
plot-method | Diagnostic Plots for Binding Site Scores |
plot-method | Diagnostic Plots for Read Counts |
pos2gff | Convert genome coordinates into GFF format |
pvalue | Access slots of S4 classes |
pvalue-method | Access slots of S4 classes |
pvalue-methods | Access slots of S4 classes |
range-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-method | Class "ReadCounts" |
score | Access slots of S4 classes |
score-method | Class "BindScore" |
simpleNucCall | Predict nucleosome positions from high-throughput sequencing data |
startScore | Score potential protein binding sites |
strandPileup | Strand specific read counts |
strandPileup-method | Strand specific read counts |
strandPileup-methods | Strand specific read counts |
support | Access slots of S4 classes |
support-method | Class "BindScore" |
support-method | Access slots of S4 classes |
support-methods | Access slots of S4 classes |
tail-method | Class "BindScore" |
windowCounts | Summarize read counts in a sliding window |
$-method | Class "ReadCounts" |
$<--method | Class "ReadCounts" |
[-method | Class "BindScore" |
[-method | Class "ReadCounts" |
[<--method | Class "ReadCounts" |
[[-method | Class "BindScore" |
[[-method | Class "ReadCounts" |
[[<--method | Class "ReadCounts" |