Showing 9 of 9 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

  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

  GRIT — source

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

  Software type: peak caller

• Software

  released

  GEM — source

  GEM is a Java software package for analyzing genome wide ChIP-seq/ChIP-exo data. GEM can decompose single observed peaks into multiple binding events, determine binding event location at high spatial resolution, and discover explanatory DNA sequence motif

  Software type: peak caller

• Software

  released

  PeakSeq — source

  Identifies enriched regions in ChIP-seq type experiments and explicitly compares signal experiments to control experiments. PeakSeq will be used in the ENCODE 3 uniform peak calling 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