Showing 22 of 22 results

• Software

  released

  dnase-align-bwa-pe — source

  Aligns paired-end reads by BWA for DNase ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  DNase Pipeline — source

  Repository for Uniform processing of DNase Hypersensitivity (DNaseHS) and Digital Genomic Footprinting (DGF) though pipelines as implemented by the ENCODE DCC.

• Software

  released

  dnase-align-bwa-se — source

  Aligns single-end reads by BWA for DNase ENCODE uniform processing pipeline.

  Software type: aligner

• 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-filter-se — source

  Merges and filters single-end aligned reads for DNase ENCODE uniform processing pipeline.

  Software type: filtering

• Software

  released

  hotspot2 — source

  Hotspot2 replaces the previous long running hotspot package.

  Software type: peak caller

• Software

  released

  trim-adapters-illumina — source

  This program will trim adapters from pair-end sequencing tags produced using the Illumina(c) platform.

  Software type: filtering

• Software

  released

  modwt — source

  A very efficient implemenation of the the Maximal Overlap Discrete Wavelet Tranform (MODWT). See D. B. Percival and A. T. Walden (2000), Wavelet Methods for Time Series Analysis. Cambridge, England: Cambridge University Press. This is not the usual discre

• 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-filter-pe — source

  Merges and filters paired-end aligned reads for quality and UMI duplicates for DNase ENCODE uniform processing pipeline.

  Software type: filtering

• Software

  released

  F-seq — source

  F-seq is a software package that generates a continuous density estimation of sequence tags mapped to a reference genome, which can be displayed using the UCSC Genome Browser. The continuous density plots are more intuitive than discrete histogram-like pl

  Software type: peak caller

• Software

  released

  Wiggler — source

  Produces normalized genome-wide signal coverage tracks from raw read alignment files. Allows pooling of replicate datasets while allowing for replicate and data-type specific read shifting and smoothing parameters. It can be used to generate signal densit

• 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

  BWA — source

  BWA is a software package for mapping low-divergent sequences based on a Burrows-Wheeler index against a large reference genome, such as the human genome. Publications for the short read alignment component is found at PMID: 19451168, while PMID: 2008050

  Software type: aligner

• 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

  dnase-index-bwa — source

  Indexes the reference genome by BWA, and processes mappability and blacklist for DNase ENCODE uniform processing pipeline.

  Software type: other

• Software

  released

  StamPipes

  This is a focused collection of makefiles and scripts to for analysis on Illumina sample data. While this probably can't be directly used by someone not in our lab, it might be a useful reference for others.

  Software type: filtering

• Software

  released

  dnase-call-hotspots — source

  Calls hotspots and peaks on filtered alignments by hotspot2 for DNase ENCODE uniform processing pipeline.

  Software type: peak caller

• Software

  released

  dnase-density

  Generates normalized density signal from aligned and filtered reads for DNase ENCODE uniform processing pipeline.

  Software type: file format conversion

• Software

  released

  chromCor.Rscript — source

  Calculates correlation between two replicate DNase signals.

  Software type: quality metric

• Software

  released

  BEDTools — source

  Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetics: that is, set theory on the genome. For example, bedtools allows one to intersect, merge

  Software type: file format conversion

• Software

  released

  SPP — source

  A ChIP-seq peak calling algorithm, implemented as an R package, that accounts for the offset in forward-strand and reverse-strand reads to improve resolution, compares enrichment in signal to background or control experiments, and can also estimate whethe

  Software type: peak caller