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recoup (version 1.0.2)

An R package for the creation of complex genomic profile plots

Description

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

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Version

Version

1.0.2

License

GPL (>= 3)

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Repository

https://github.com/pmoulos/recoup

Maintainer

Panagiotis Moulos

Last Published

February 15th, 2017

Functions in recoup (1.0.2)

Annotation downloader

Get and set some reusable objects from a recoup object

Plot list objects returned by recoup

Apply k-means clustering to profile data

List default Ensembl biotypes

recoup_test_data

Reference and genomic sample regions for recoup testing

Create genomic signal profiles in predefined or custom areas using short sequence reads

Remove data from recoup list object

preprocessRanges

Read and preprocess BAM/BED files to GRanges

Calculate coverages over a genomic region

Plot (faceted) average genomic coverage profiles

Calculate final profile matrices for plotting

recoupCorrelation

Plot (faceted) average genomic coverage correlations

Plot genomic coverage heatmaps

buildAnnotationStore

Build a local annotation database for recoup

Calculate coverage in a set of reference genomic regions (RNA-Seq or spliced mode)

Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode)

Subset recoup output list objects