Galaxy |

IDR (version 2.0.3)

First set of peaks in GFF or BED format:

Second set of peaks in GFF or BED format:

List of peaks to filter by:

Input BED format:

This option is ignored if the input file is GFF

Column to use for ranking peaks:

idr_threshold:

soft_idr_threshold:

Output PNG plot of peaks:

Use peaks without an overlapping match and set the value to 0:

Method to use for merging peaks:

Initial value of mu:

Initial value of sigma:

Initial value of rho:

Initial value of the mixture parameters:

Fix mu to the starting point and do not let it vary:

Fix sigma to the starting point and do not let it vary:

Allow signal points that are below the noise mean:

Set the IDR value for a group of multi summit peaks:

A group of peaks with the same chr/start/stop but different summits

Allow negative values for scores:

The random seed value:

The maximum number of optimization iterations:

The maximum change in parameter value changes for convergence:

Only return the merged peak list:

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates.