Showing 5 of 5 results

• Software

  released

  dnase-rep-corr — source

  Calculated correlation beteen two replicate signals for DNase ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  dnase-qc-bam

  Evaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  Irreproducible Discovery Rate (IDR) — source

  Measures consistency between replicates in high-throughput experiments. Also uses reproducibility in score rankings between peaks in each replicate to determine an optimal cutoff for significance. The core IDR R package can be downloaded from the IDR do

  Software type: quality metric, filtering

• Software

  released

  Phantompeakqualtools — source

  Used to generate three quality metrics: NSC, RSC, and PBC. The NSC (Normalized strand cross-correlation) and RSC (relative strand cross-correlation) metrics use cross-correlation of stranded read density profiles to measure enrichment independently of pe

  Software type: quality metric, filtering

• Software

  released

  chromCor.Rscript — source

  Calculates correlation between two replicate DNase signals.

  Software type: quality metric