Showing 18 of 18 results

• Software

  released

  Genotype QC and imputation: eQTL-Catalogue/genimpute — source

  Genotype QC and imputation: eQTL-Catalogue/genimpute. Genotype imputation and quality control workflow used by the eQTL Catalogue.

  Software type: quality metric

• Software

  released

  SPOT (Signal Portion of Tags) — source

  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 metric

• Software

  released

  dnase-rep-corr — source

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

  Software type: quality metric

• 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

  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

  dnase-eval-bam — source

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

  Software type: quality metric

• Software

  released

  edwBamStats — source

  Collect some basic characterization statistics of a BAM file.

  Software type: quality metric

• Software

  released

  CpG methylation correlation — source

  Calculates spearman correlation of 2 replicate bedmethyl files of CpG methylation.

  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

• Software

  released

  npIDR — source

  Non-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. Ori

  Software type: quality metric

• Software

  released

  FastQC — source

  FastQC 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 pr

  Software type: quality metric

• Software

  released

  chromCor.Rscript — source

  Calculates correlation between two replicate DNase signals.

  Software type: quality metric

• Software

  released

  CLIPper — source

  A tool to detect CLIP-seq peaks. The Yeo lab describes their CLIP-seq cluster-identification algorithm on PMID: 24213538

  Software type: quality metric, peak caller