Title: RnaChipIntegrator-0.4.3

Type Software Peter Briggs, Ian Donaldson, Leo Zeef (2014): RnaChipIntegrator-0.4.3. Zenodo. Software. https://zenodo.org/record/11036

Authors: Peter Briggs (University of Manchester) ; Ian Donaldson (University of Manchester) ; Leo Zeef (University of Manchester) ; Casey Bergman (University of Manchester) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

RnaChipIntegrator is a software utility that performs integrated analyses of gene expression and ChIP data, identifying the nearest ChIP peaks to each transcript, and vice versa. Output of RnaChipIntegrator differs according to the criteria that are used to calculate the distances between ChIP peaks and transcripts.

While the program was originally intended specifically for ChIP-Seq and RNA-Seq data the approach works equally well for ChIP-chip and microarray expression data, and can also be used to integrate any set of genomic features (e.g. canonical genes, CpG islands) with expression data.

Changes in this version:

Adds a new output option --pad: for NearestTranscriptsToPeakEdge and NearestTSSToPeakEdge analyses, where necessary adds "blank" lines (i.e. only containing chromosome, start and end) to output files and spreadsheet so that each reported peak has the same number of lines associated regardless of the number of hits.

Truncate worksheet titles if they exceed maximum length as defined by the spreadsheet writing libraries.

More information

• DOI: 10.5281/zenodo.11036

Dates

• Publication date: 2014
• Issued: July 25, 2014

Rights

• https://opensource.org/licenses/artistic-license-2.0 Artistic License 2.0
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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