Showing 10 of 10 results

• Software

  released

  Single Cell ATAC Software — source

  Cell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Single Cell ATAC data produced by the 10x Genomics Chromium platform.

  Software type: peak caller

• Software

  released

  Altius-Index

  Method for generating a master list / Index of DNaseI-Hypersensitive Sites ("consensus DHSs"). All code, implementation details and design by Wouter Meuleman and Eric Rynes. Docker implementation by Jemma Nelson.

  Software type: peak caller

• Software

  released

  Mango — source

  Mango: a bias-correcting ChIA-PET analysis pipeline

  Software type: peak caller

• Software

  released

  hotspot2 — source

  Hotspot2 replaces the previous long running hotspot package.

  Software type: peak caller

• Software

  released

  rampage-peaks — source

  Peak calling by GRIT for Rampage ENCODE uniform processing pipeline.

  Software type: peak caller

• Software

  released

  overlap_peaks.py — source

  overlap_peaks.py is a method to select overlapping peaks among replicates and psuedo-replicates

  Software type: peak caller

• 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

  GRIT — source

  Generalized RNA Integration Tool: Transcript prediction utilizing RNA-seq and gene boundary information.

  Software type: peak caller

• 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

  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