r3Cseq specifications

Information


Unique identifier OMICS_01560
Name r3Cseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for r3Cseq

r3Cseq in publications

 (7)
PMCID: 5833835
PMID: 29422670
DOI: 10.1038/s41419-017-0173-6

[…] analysis, the adapter sequences were first removed using cutadapt software in samtools. bowtie was used to map the reads to the human hg19 assembly. then, the mapped data were processed using the r3cseq package in r 3.3.1 using rpm normalization., the gata2 interaction genomic loci were viewed in the ucsc genome browser, and the bac ends track was enabled to facilitate the determination […]

PMCID: 5438348
PMID: 28526829
DOI: 10.1038/s41598-017-02257-3

[…] the viewpoint sequence was removed by tagdust2 and the processed read was mapped by bowtie2 and over 80% of each library could be mapped to the hg19 genome. the mapped 4c-seq data was analysed by r3cseq., 2 million cells were fixed with 1% formaldehyde in pbs for 10 minutes at room temperature. the fixation reaction was quenched by adding glycine to 0.25 m final concentration. the cell pellet […]

PMCID: 5316867
PMID: 28195176
DOI: 10.1038/ncomms14418

[…] analysis., the reads from each library were parsed based on the bait-specific primer sequence and mapped to the reduced hg19 genome using bwa-aln with the default parameters. a bioconductor package ‘r3cseq' (ref. ) with 2.5 kb sliding window was used to determine significant interactions and calculate interaction difference., tfs binding differentially to the 116 loci were annotated to panther […]

PMCID: 5659820
PMID: 28949289
DOI: 10.7554/eLife.28590.019

[…] the very-sensitive flag 3. alignments were filtered with a mapping quality (mapq) score >30 to select for high-confidence alignments using samtools (). contacts were then normalized using the r3cseq r package and assigned false discovery rate q-values to interactions, with the aim of finding those significantly over-represented relative to expectation. the normalization procedure for 4c […]

PMCID: 5052795
PMID: 27677335
DOI: 10.1038/ncomms12983

[…] we probed multiple genomic locations (n=92, referred to as ‘capture points') across the 36 predicted super-enhancers, identifying 88 capture points with significant interactions (q<0.05, r3cseq package). depicts 12 representative predicted super-enhancers covering 20 capture points. on average, each predicted super-enhancer exhibited 20–26 and 5–7 interactions with other genomic […]


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r3Cseq institution(s)
Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway

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