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universalmotif - Import, Modify, and Export Motifs with R

A comprehensive toolkit for working with sequence motifs in R. Imports and exports most common motif formats (JASPAR, MEME, HOMER, TRANSFAC, CIS-BP, UNIPROBE) and interoperates with the other Bioconductor motif packages. Analysis functions cover de novo motif discovery, motif-vs-motif comparison and clustering, P-value calculation, sequence scanning, enrichment against shuffled or composition-matched backgrounds, positional bias testing, and pairwise motif co-occurrence. Also includes utilities for sequence shuffling, motif trimming, higher-order representations, ground-truth simulation by motif implantation, and logo-plotting functionality.

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motifannotationmotifdiscoverydataimportgeneregulationmotif-analysismotif-enrichment-analysissequence-logocpp

11.90 score 33 stars 14 dependents 588 scripts 2.1k downloads

quaqcr - Quick ATAC-Seq QC

A wrapper around the 'quaqc' program described in Tremblay and Questa (2024) <doi:10.1093/bioinformatics/btae649>. 'quaqc' allows for assay for transposase-accessible chromatin using sequencing (ATAC-seq) specific quality control and read filtering of next-generation sequencing (NGS) data with minimal processing time and extremely low memory overhead. Any number of samples can be processed, using multiple threads if desired. 'quaqc' outputs a comprehensive set of aligned read metrics, including alignment size, fragment size, percent duplicates, mapq scores, read depth, GC content, and others. Although designed for ATAC-seq data, 'quaqc' can also be used for other unspliced DNA sequencing experiments (such as chromatin immunoprecipitation sequencing, or ChIP-seq) as many of the metrics are related to general sequencing quality. This R package also provides additional utilities for custom analyses and plotting of 'quaqc' results.

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3.00 score 1 stars 2 scripts 79 downloads

quaqcr - Quick ATAC-Seq QC

A wrapper around the 'quaqc' program described in Tremblay and Questa (2024) <doi:10.1093/bioinformatics/btae649>. 'quaqc' allows for assay for transposase-accessible chromatin using sequencing (ATAC-seq) specific quality control and read filtering of next-generation sequencing (NGS) data with minimal processing time and extremely low memory overhead. Any number of samples can be processed, using multiple threads if desired. 'quaqc' outputs a comprehensive set of aligned read metrics, including alignment size, fragment size, percent duplicates, mapq scores, read depth, GC content, and others. Although designed for ATAC-seq data, 'quaqc' can also be used for other unspliced DNA sequencing experiments (such as chromatin immunoprecipitation sequencing, or ChIP-seq) as many of the metrics are related to general sequencing quality. This R package also provides additional utilities for custom analyses and plotting of 'quaqc' results.

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1.70 score 2 scripts