Genomic region overlap analysis software tools | DNA annotation
A common question in genomic analysis is whether two sets of genomic intervals overlap significantly. This question arises, for example, when interpreting ChIP-Seq or RNA-Seq data in functional terms. Because genome organization is complex, answering this question is non-trivial.
A method for identifying whether two sets of intervals are spatially correlated across a genome, detected as a deviation from a nonuniform distribution of one set of intervals with respect to the other. GenometriCorr performs all analyses on each input, so that a variety of biologically significant relationships are queried. This includes looking for proximity, looking for uniform spacing, looking for increased or decreased overlaps of intervals or points, and presenting the data in a way that a biologist can understand.
Investigates and handles high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. GenomicTools can be used to conduct alignments to reference genome, scan computations or shuffle within a reference set of regions. It serves for a wide spectrum of tasks ranging from pre-processing and quality control to meta-analyses. This tool is able to reduce the memory requirements for large datasets study.
Aims to facilitate the analysis of genome scale data from several standard file formats. CGAT permits users to filter, compare, convert, summarize and annotate genomic intervals, gene sets and sequences. The software comprises more than 50 tagged tools, each with documentation and examples. The tags associate tools with broad themes (genomic intervals, gene sets, sequences), standard genomic file formats and the type of computation performed by the tool, such as statistical summary, format conversion, annotation, comparison or filtering.
An R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is a customizable tool to manage and analyze sets of regions, and a useful addition to the NGS and genome wide analysis toolbox.
Enables flexible genomic interval analysis. valr is a program that permits manipulation of data in R. This tool provides a set of functions to read BED, BEDgraph, and VCF formats into R. It also includes features to support connections to remote databases to access the UCSC and Ensembl databases. Moreover, it can be used in RMarkdown documents to provide documentation of exploratory data analyses and generate reproducible work-flows for data processing.
Allows integrative context-dependent analyses of diverse local and remotely hosted datasets, as well as annotation and spatial querying. CruzDB is a parallelizable programmatic interface with University of California, Santa Cruz (UCSC) genome browser that offers a syntax to address common use-cases including annotation and spatial querying. The software can be used for any organism and version available in the UCSC database.
Estimates genome-wide positional correlations. StereoGene is able to rapidly compute correlations of continuous genome-wide features in addition to discrete gene intervals used in most correlation techniques. It is applicable for analysis of similarity of genomic-track-represented biological data, including massive analysis. The tool provides a collection of genome-wide correlation techniques.