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Chromosome conformation capture-on-chip analysis bioinformatics software tools

4C involves PCR amplification of DNA fragments cross-linked and ligated to a DNA restriction fragment of choice (here,HindIII fragments). Typically, this yields a pattern of PCR fragments specific for a given tissue and highly reproducible between…
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w4CSeq
Web
Desktop

w4CSeq

A command line software tool and a web interface, which takes in the raw 4C…

A command line software tool and a web interface, which takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis and presents results in a user-friendly…

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fourSig
Desktop

fourSig

A suite of programs for analyzing and visualizing 4C-seq data. fourSig can…

A suite of programs for analyzing and visualizing 4C-seq data. fourSig can analyze data from a wide variety of 4C-seq protocols, uses the full range of quantitative information captured by 4C-seq,…

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FourCSeq
Desktop

FourCSeq

A package dedicated to the analysis of (multiplexed) 4C sequencing data.…

A package dedicated to the analysis of (multiplexed) 4C sequencing data. FourCSeq provides a pipeline to detect specific interactions between DNA elements and identify differential interactions…

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Basic4Cseq
Desktop

Basic4Cseq

A package for basic filtering, analysis and subsequent near-cis visualization…

A package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Basic4Cseq processes aligned 4C-seq raw data stored in binary alignment/map (BAM) format and maps the…

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4C-ker
Desktop

4C-ker

A hidden-Markov model based analysis that identifies regions throughout the…

A hidden-Markov model based analysis that identifies regions throughout the genome that interact with the 4C bait locus. In addition we incorporate methods for the identification of differential…

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Scale4C
Desktop

Scale4C

Allows scale-space transformation. Scale4C is a useful tool to visualize 4C-seq…

Allows scale-space transformation. Scale4C is a useful tool to visualize 4C-seq data. It is based on Gauss kernels of increasing sigma to smooth the original 4C-seq signal. The tool contains…

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