ENCODE Software
All software used or developed by the ENCODE Consortium
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- dnase-qc-bamEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: quality metric
- chromCor.Rscript — sourceCalculates correlation between two replicate DNase signals.Software type: quality metric
- dnase-rep-corr — sourceCalculated correlation beteen two replicate signals for DNase ENCODE uniform processing pipeline.Software type: quality metric
- dnase-eval-bam — sourceEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: quality metric
- edwBamStats — sourceCollect some basic characterization statistics of a BAM file.Software type: quality metric
- rampage-mad-qc — sourceMean Absolute Deviation (MAD) and correlation calculated from two replicates for Rampage ENCODE uniform processing pipeline.Software type: quality metric
- srna-mad-qc — sourceMean Absolute Deviation (MAD) and correlation calculated from two replicates for small-RNA-seq ENCODE uniform processing pipeline.Software type: quality metric
- lrna-mad-qc — sourceMean Absolute Deviation (MAD) and correlation calculated from two replicates for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: quality metric
- rampage-idr — sourceIrreproducible Discovery Rate (IDR) calculation from two replicates for Rampage ENCODE uniform processing pipeline.Software type: quality metric
- CpG methylation correlation — sourceCalculates spearman correlation of 2 replicate bedmethyl files of CpG methylation.Software type: quality metric
- Median Absolute Deviation — sourceCalculates 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
- npIDR — sourceNon-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 metric
- FastQC — sourceFastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. Babraham Bioinformatics Web site, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Software type: quality metric
- SPOT (Signal Portion of Tags) — sourceMeasures 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 metric
- Phantompeakqualtools — sourceUsed to generate these quality metrics: NSC and RSC. 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.Software type: quality metric, filtering
- Irreproducible Discovery Rate (IDR) — sourceMeasures 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.htmlSoftware type: quality metric, filtering