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FourCSeq specifications

Information


Unique identifier OMICS_08435
Name FourCSeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
methods, Biobase, GenomicRanges, Rsamtools, Matrix, splines, Biostrings, fda, rtracklayer, BiocStyle, GenomicAlignments, SummarizedExperiment, ggplot2, DESeq2, gtools, knitr, R(>=3.0), reshape2, TxDb.Dmelanogaster.UCSC.dm3.ensGene, DESeq2(>=1.9.11), ggbio, LSD
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Felix A. Klein

Publication for FourCSeq

FourCSeq citations

 (5)
library_books

CTCF counter regulates cardiomyocyte development and maturation programs in the embryonic heart

2017
PLoS Genet
PMCID: 5591014
PMID: 28846746
DOI: 10.1371/journal.pgen.1006985

[…] sites per window). the frequency of captured sites per window was used to fit a distance decreasing monotone function and z-scores were calculated from its residuals using a modified version of fourcseq []. significant contacts were considered in cases where the z-score was >2 in both replicates and deviated significantly (adjusted p value <0.05) from its normal cumulative […]

library_books

Functional characterisation of cis regulatory elements governing dynamic Eomes expression in the early mouse embryo

2017
PMCID: 5399628
PMID: 28174238
DOI: 10.1242/dev.147322

[…] in activation of the eomes target genes, lhx1 and foxa2 (fig. s7c) (; )., ng capture-c using viewpoints from the pse_a and pse_b exhibited promoter interactions in esc (fig. s8) when analysed with fourcseq (). these interactions were marginally reduced in de. however, the overall change was not statistically significant. by contrast, ng capture-c revealed significant interactions […]

library_books

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

2016
Mol Syst Biol
PMCID: 5199122
PMID: 27940490
DOI: 10.15252/msb.20167311

[…] revealed extensive similarities, especially within the viewpoint's tad (fig d). few contacts were seen only in the absence of cross‐linking (which was also confirmed by a differential analysis via “fourcseq”; klein et al, ; ). compared to high‐resolution hi‐c (rao et al, ) and chia‐pet contact maps (papantonis et al, ) from huvecs, i4c showed matching interaction profiles and aligned well […]

library_books

Nuclear Architecture Organized by Rif1 Underpins the Replication Timing Program

2016
Mol Cell
PMCID: 4724237
PMID: 26725008
DOI: 10.1016/j.molcel.2015.12.001

[…] by 3c-qpcr (f). second, we used 3d fluorescence in situ hybridization (fish) to validate the increased proximity of one of the contacts (g). third, an independent analysis of the 4c-seq data with fourcseq () (see ) (), confirmed a consistent difference between the two conditions. altogether, these results establish rif1 as a spatial organizer of chromatin., the loosening of spatial control […]

library_books

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

2015
Nat Methods
PMCID: 4724891
PMID: 26595209
DOI: 10.1038/nmeth.3664

[…] based data, such as the bioconductor package deseq2. we compared the effectiveness of this approach at identifying known regulatory elements with two tools commonly used for 3c analysis (, - and ), fourcseq and r3c-seq which also use replicates and comparative analysis but additionally normalise for genomic distance using different models. we tested all approaches on the well-characterized test […]


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FourCSeq institution(s)
European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany

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