Man pages for sarks
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
| blockInfo | Get sarks smoothed scores for input sequence |
| blockScores | SArKS input scores |
| clusterCounts | Count occurrences of k-mer clusters |
| clusterKmers | Cluster k-mers |
| estimateFalsePositiveRate | Estimating SArKS false positive rate |
| extendKmers | Extend k-mers in length where possible |
| kmerCounts | Count occurrences of k-mer |
| kmerPeaks | Call k-mer peaks |
| locateClusters | Locate occurrences of specified clusters of k-mers |
| locateKmers | Locate occurrences of specified k-mers |
| mergedKmerSubPeaks | Identify and merge k-mer sub-peaks within multi-motif domains |
| permutationDistribution | Estimating distribution of maximum smoothed sequence scores... |
| permutationThresholds | Set smoothed score thresholds based on permutation... |
| pruneIntervals | Prune nested k-mer intervals from called k-mer peak set. |
| regexCounts | Count occurrences of regular expression |
| regexLocate | Locate occurrences of regular expression |
| Sarks | Suffix Array Kernel Smoothing |
| sarksFilters | Smoothing window and Gini impurity filter settings |
| simulatedScores | Scores associated with simulated sequences from SArKS paper. |
| simulatedSeqs | Simulated sequences from SArKS paper. |
| sourceBlock | Identify associated input sequence for given position(s) in... |
