Showing 8 of 8 results
Software
released
Measures signal-to-noise in genome-wide epigenetic profiling assays by calculating the fraction of reads that fall in tag-enriched regions (see the Hotspot program) from a sample of 5 million reads. The SPOT methodology can be generalized to use any peak-Software type: quality metricSoftware
released
Mean Absolute Deviation (MAD) and correlation calculated from two replicates for Rampage ENCODE uniform processing pipeline.Software type: quality metricSoftware
released
Mean Absolute Deviation (MAD) and correlation calculated from two replicates for small-RNA-seq ENCODE uniform processing pipeline.Software type: quality metricSoftware
released
Mean Absolute Deviation (MAD) and correlation calculated from two replicates for long-RNA-seq ENCODE uniform processing pipeline.Software type: quality metricSoftware
released
Collect some basic characterization statistics of a BAM file.Software type: quality metricSoftware
released
Irreproducible Discovery Rate (IDR) calculation from two replicates for Rampage ENCODE uniform processing pipeline.Software type: quality metricSoftware
released
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 doSoftware type: quality metric, filteringSoftware
released
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 peSoftware type: quality metric, filtering