#### Showing 12 of 12 results

Software

releasedEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.**Software type:**quality metricSoftware

releasedCalculates correlation between two replicate DNase signals.**Software type:**quality metricSoftware

releasedCalculated correlation beteen two replicate signals for DNase ENCODE uniform processing pipeline.**Software type:**quality metricSoftware

releasedCollect some basic characterization statistics of a BAM file.**Software type:**quality metricSoftware

releasedMean Absolute Deviation (MAD) and correlation calculated from two replicates for Rampage ENCODE uniform processing pipeline.**Software type:**quality metricSoftware

releasedMean Absolute Deviation (MAD) and correlation calculated from two replicates for small-RNA-seq ENCODE uniform processing pipeline.**Software type:**quality metricSoftware

releasedMean Absolute Deviation (MAD) and correlation calculated from two replicates for long-RNA-seq ENCODE uniform processing pipeline.**Software type:**quality metricSoftware

releasedIrreproducible Discovery Rate (IDR) calculation from two replicates for Rampage ENCODE uniform processing pipeline.**Software type:**quality metricSoftware

releasedNon-parametric Irreproducibe Detection Rate (npIDR) essentially takes a pooled sample of all replicas and computes (a) the frequency of seeing count=x; (b) the frequency of seeing count=x given that in *ALL* other replicas the count is equal to zero. Original Irreproducible detection rate statistical test published (DOI: 10.1214/11-AOAS466).**Software type:**quality metricSoftware

releasedMeasures 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-finder. A publication of SPOT and a more complete description are in preparation. SPOT is simply the percentage of all tags that fall in hotspots, and the publication for the Hotspot quality metric is found at PMID: 21258342.**Software type:**quality metricSoftware

releasedUsed 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 peak calling. The PBC (PCR bottleneck coefficient) is an approximate measure of library complexity. PBC is the ratio of (non-redundant, uniquely mappable reads)/(uniquely mappable reads).**Software type:**quality metric, filteringSoftware

releasedMeasures 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 download page: http://cran.r-project.org/web/packages/idr/index.html**Software type:**quality metric, filtering