r-cran-spp

GNU R ChIP-seq processing pipeline

Description

R package for anlaysis of ChIP-seq and other functional sequencing data

* Assess overall DNA-binding signals in the data and select appropriate

quality of tag alignment.

* Discard or restrict positions with abnormally high number of tags.

* Calculate genome-wide profiles of smoothed tag density and save them

in WIG files for viewing in other browsers.

* Calculate genome-wide profiles providing conservative statistical

estimates of fold enrichment ratios along the genome. These can be

exported for browser viewing, or thresholded to determine regions of

significant enrichment/depletion.

* Determine statistically significant point binding positions

* Assess whether the set of point binding positions detected at a

current sequencing depth meets saturation criteria, and if does not,

estimate what sequencing depth would be required to do so.

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