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New features in genomation package

October 15, 2015
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New features in genomation package

Extending genomation to work with paired-end BAM filesExtending genomation to work with paired-end BAM filesAccelerate functions responsible for reading genomic filesParallelizing data processing in ScoreMatrixListArithmetic, indicator and logic operations as well as subsetting work on ScoreMatrix objectsImprovements and new arguments in visualization functionsFaster heatmapsNew clustering possibilities in heatmaps: “clustfun” argument in multiHeatMatrixDefining which matrices are used for clustering: “clust.matrix”...

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New features in genomation package

October 15, 2015
By
New features in genomation package

Extending genomation to work with paired-end BAM files Extending genomation to work with paired-end BAM files Accelerate functions responsible for reading genomic files Parallelizing data processing in ScoreMatrixList Arithmetic, indicator and logic operations as well as subsetting work on ScoreMatrix objects Improvements and new arguments in visualization functions Faster heatmaps New clustering possibilities in heatmaps: “clustfun” argument in multiHeatMatrix Defining which matrices are used for clustering: “clust.matrix”...

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Comparing the execution time between foverlaps and findOverlaps

April 13, 2015
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Comparing the execution time between foverlaps and findOverlaps

Both of these functions find overlaps between genomic intervals. The findOverlaps function is from the Bioconductor package GenomicRanges(or IRanges if you don't need to compare intervals with an associated chromosome and strand). foverlaps is from th...

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Comparing the execution time between foverlaps and findOverlaps [data.table vs GenomicRanges]

April 13, 2015
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Comparing the execution time between foverlaps and findOverlaps [data.table vs GenomicRanges]

Both of these functions find overlaps between genomic intervals. The findOverlaps function is from the Bioconductor package GenomicRanges(or IRanges if you don't need to compare intervals with an associated chromosome and strand). foverlaps is from the data.tablepackage and is inspired by findOvelaps. In genomics, we often have one large data set X with small interval ranges (usually sequenced...

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Using genomation to analyze methylation profiles from Roadmap epigenomics and ENCODE

March 31, 2015
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Using genomation to analyze methylation profiles from Roadmap epigenomics and ENCODE

The genomation package is a toolkit for annotation and visualization of various genomic data. The package is currently in developmental version of BioC. It allows to analyze high-throughput data, including bisulfite sequencing data. Here, we will visualize the distribution of CpG methylation around promoters and their locations within gene structures on human chromosome 3.Heatmap and plot of meta-profiles of...

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