r3Cseq 1.38.0 – Discovery of Long-range Genomic Interactions from Chromosome Conformation Capture and Next-generation Sequencing data

r3Cseq 1.38.0

:: DESCRIPTION

r3Cseq is an R package designed to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. r3Cseq was designed to perform data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

::DEVELOPER

Supat Thongjuea 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX / Windows
  • R package

:: DOWNLOAD

 r3Cseq

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(13):e132. doi: 10.1093/nar/gkt373. Epub 2013 May 13.
r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B.

GIVE v0.2.0 – Genomic Interaction Visualization Engine

GIVE v0.2.0

:: DESCRIPTION

GIVE is an open source programming library that allows anyone without much programming experience to build custom genome browser websites or apps. With a few lines of codes, one can set up GIVE service on a local machine, manage custom data and build an interactive genome browser.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Web Server

:: DOWNLOAD

GIVE

:: MORE INFORMATION

Citation

GIVE: portable genome browsers for personal websites.
Cao X, Yan Z, Wu Q, Zheng A, Zhong S.
Genome Biol. 2018 Jul 18;19(1):92. doi: 10.1186/s13059-018-1465-6.