Tag: ChIA-PET

Mango 1.0.3 – ChIA-PET Analysis Software

Mango 1.0.3

:: DESCRIPTION

Mango is a complete ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag sequencing) data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.

::DEVELOPER

Mango team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Bowtie
  • Bedtools
  • MACS2

:: DOWNLOAD

 Mango

:: MORE INFORMATION

Citation

Mango: A bias correcting ChIA-PET analysis pipeline.
Phanstiel DH, Boyle AP, Heidari N, Snyder MP.
Bioinformatics. 2015 Jun 1. pii: btv336.

MICC 1.0 – Model based Interaction Calling from ChIA-PET data

MICC 1.0

:: DESCRIPTION

MICC is an R package which provides methods to detect chromatin interactions from ChIA-PET data.

::DEVELOPER

MICC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

 MICC

:: MORE INFORMATION

Citation

MICC: an R package for identifying chromatin interactions from ChIA-PET data.
He C, Zhang MQ, Wang X.
Bioinformatics. 2015 Jul 31. pii: btv445.

ChIA-PET 1.0 – Processing of ChIA-PET sequence data

ChIA-PET 1.0

:: DESCRIPTION

ChIA-PET Tool  is a software package for automatic processing of ChIA-PET (Chromatin Interaction Analysis using Paired-End Tag sequencing )sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser

:: DEVELOPER

the Genome Institute of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apach
  • MySQL
  • PHP
  • Java
  • R package
  • C Compiler

:: DOWNLOAD

 ChIA-PET 

:: MORE INFORMATION

Citation

ChIA-PET analysis of transcriptional chromatin interactions.
Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.
Methods. 2012 Nov;58(3):289-99.