Showing 11 of 11 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

  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

  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