as.list,AlignedRead-method |
A function to read in Aligned Short Reads |
basesCovered |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
coerce,AlignedRead,GenomeData-method |
A function to read in Aligned Short Reads |
combineLanes |
Combine or subsample short read alignment locations |
contextDistribution |
Tabulate peak locations according to genomic context |
copyIRanges |
Associate ranges to coverage. |
copyIRangesbyChr |
Associate ranges to coverage. |
coverageplot |
Plot coverage on a small interval. |
cstest |
A test ChIP-Seq dataset |
densityCorr |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
diffPeakSummary |
A function to identify and produce summary statistics for differentially expressed peaks. |
estimate.mean.fraglen |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
estimate.mean.fraglen,AlignedRead-method |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
estimate.mean.fraglen,GenomeData-method |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
estimate.mean.fraglen,IntegerList-method |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
estimate.mean.fraglen,list-method |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
estimate.mean.fraglen,RangedData-method |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
estimate.mean.fraglen,RangesList-method |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
extendReads |
A function to extend short reads. |
genomic_exons |
(Deprecated) Functions that compute genomic regions of interest. |
genomic_introns |
(Deprecated) Functions that compute genomic regions of interest. |
genomic_regions |
(Deprecated) Functions that compute genomic regions of interest. |
laneSubsample |
Combine or subsample short read alignment locations |
readReads |
A function to read in Aligned Short Reads |
sparse.density |
Estimate summaries of the distribution of fragment lengths in a
short-read experiment. The methods are designed for ChIP-Seq
experiments and may not work well in data without peaks. |
subsetSummary |
Compute summaries for cumulative subsets of a short-read data set. |