sarks
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
Bioconductor version: Release (3.20)
Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.
Author: Dennis Wylie [aut, cre] 
Maintainer: Dennis Wylie <denniscwylie at gmail.com>
citation("sarks")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sarks")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sarks")| sarks-vignette | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, FeatureExtraction, GeneExpression, GeneRegulation, MotifDiscovery, RNASeq, Software, Transcriptomics |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | rJava, Biostrings, IRanges, utils, stats, cluster, binom |
| System Requirements | Java (>= 1.8) |
| URL | https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797 https://github.com/denniscwylie/sarks |
| Bug Reports | https://github.com/denniscwylie/sarks/issues |
See More
| Suggests | RUnit, BiocGenerics, ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sarks_1.18.0.tar.gz |
| Windows Binary (x86_64) | sarks_1.18.0.zip |
| macOS Binary (x86_64) | sarks_1.18.0.tgz |
| macOS Binary (arm64) | sarks_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sarks |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sarks |
| Bioc Package Browser | https://code.bioconductor.org/browse/sarks/ |
| Package Short Url | https://bioconductor.org/packages/sarks/ |
| Package Downloads Report | Download Stats |