Tag: Peak-caller

PeakRanger 1.18 – Multi-purpose, ultrafast ChIP Seq Peak Caller

PeakRanger 1.18

:: DESCRIPTION

PeakRanger detects enriched regions from ChIP-Seq experiments and also detect summits within these regions. The software is faster than most existing peak callers while consuming less memories.

::DEVELOPER

developed in Dr.Lincoln Stein’s lab at OICR and is now in continual development at Dr.Helen Hobbs’s lab of the McDermott Center of UT Southwestern.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 PeakRanger

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 9;12:139. doi: 10.1186/1471-2105-12-139.
PeakRanger: a cloud-enabled peak caller for ChIP-seq data.
Feng X, Grossman R, Stein L.

Piranha 1.2.1 – Peak-caller for CLIP- and RIP-Seq high-throughput Protein-RNA interaction data

Piranha 1.2.1

:: DESCRIPTION

Piranha is a peak-caller for CLIP- and RIP-Seq high-throughput protein-RNA interaction data. It accepts input in BED or BAM format and identifies regions of significant enrichment for reads. Piranha can also optionally incorporate additional external covariates into the peak-calling process, and identify sites of differential binding occupancy between cell types, conditions or development stages.

::DEVELOPER

The Smith Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 Piranha

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28.
Site identification in high-throughput RNA-protein interaction data.
Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD.