seqArchR - Identify Different Architectures of Sequence Elements

seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

Last updated 23 days ago

motifdiscoverygeneregulationmathematicalbiologysystemsbiologytranscriptomicsgeneticsclusteringdimensionreductionfeatureextractiondnaseqnmfnonnegative-matrix-factorizationpromoter-sequence-architecturesscikit-learnsequence-analysissequence-architecturesunsupervised-machine-learning

4.48 score 1 stars 1 packages 8 scripts 174 downloads

seqArchRplus - Downstream analyses of promoter sequence architectures and HTML report generation

seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.

Last updated 23 days ago

annotationvisualizationreportwritinggomotifannotationclustering

4.00 score 1 scripts 151 downloads