Showing 7 of 7 results

• Software

  released

  rampage-mad-qc — source

  Mean Absolute Deviation (MAD) and correlation calculated from two replicates for Rampage ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  srna-mad-qc — source

  Mean Absolute Deviation (MAD) and correlation calculated from two replicates for small-RNA-seq ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  lrna-mad-qc — source

  Mean Absolute Deviation (MAD) and correlation calculated from two replicates for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  Median Absolute Deviation — source

  Calculates the Median Absolute Deviation (MAD) and correlation of two gene quantifications from replicate RNA-seq experiments. A measure of reproducibility, inversely correlated with data quality.

  Software type: quality metric

• Software

  released

  rampage-idr — source

  Irreproducible Discovery Rate (IDR) calculation from two replicates for Rampage 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