GenPlay protocols

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GenPlay specifications

Information


Unique identifier OMICS_08292
Name GenPlay
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Julien Lajugie <>
  • person_outline Eric Bouhassira <>

Publications for GenPlay

GenPlay in pipelines

 (5)
2015
PMCID: 4479011
PMID: 25987481
DOI: 10.1038/ncomms8051

[…] in the user-provided reference vcf file., once the variants had been called, the vcf files for the ns library were phased using the vcf for family fny01 as a reference and specific functions in genplay multi-genome. once the files were phased, files (in bed format) containing the allele depth for the paternal and maternal chromosomes were generated, again using specific functions provided […]

2014
PMCID: 4006724
PMID: 24787348
DOI: 10.1371/journal.pgen.1004319

[…] and were originally from repbase., processed and raw data files have been deposited at ncbi in the geo database. accession number: gse50978, the entire dataset can be visualized in the interactive genplay environment at http://genplay.einstein.yu.edu/library/projects/timex-nascentstrands-2013/., we thank dr. benjamin audit, diana cg bouhassira and carl schildkraut for critical reading […]

2013
PMCID: 3636266
PMID: 23633960
DOI: 10.1371/journal.pgen.1003417

[…] promoters, regardless of the presence or absence of h3k27me3 ()., although most h1d and h1c signals appeared universally distributed, we identified regions enriched for h1 binding using sicer and genplay software. identified h1d and h1c enriched regions often formed broad domains (examples shown in ). annotation of h1d- and h1c- rich regions using ceas , a software designed to characterize […]

2013
PMCID: 3636266
PMID: 23633960
DOI: 10.1371/journal.pgen.1003417

[…] histone markers. genome-wide and chromosome-wide correlation coefficients were calculated, and the scatter-plots were generated using matlab., significantly enriched regions were identified using genplay or sicer v1.1 at the following parameter settings: window size = 200, gap size = 600, e-value = 1000, an effective genome size of 80% of the entire mouse genome, and q-value (fdr) = 0.001. […]

2013
PMCID: 3669306
PMID: 23741343
DOI: 10.1371/journal.pone.0064571

[…] higher than normal read-depth in all quartet members. (more refined analysis was performed subsequently to identify cnvs). the filter was created using cnvnator and the island finder algorithm of genplay. about 18.8 * 10e6 bases, that is 0.66% of the genome (assuming a genome size of 2.86*10e9 non n bases) is covered by this filter., variant recalibration was performed following the best […]


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GenPlay in publications

 (5)
PMCID: 4479011
PMID: 25987481
DOI: 10.1038/ncomms8051

[…] efficiency in an allele-specific manner, we used the gatk software to call the single-nucleotide polymorphisms (snps) and small insertion and deletions (indels) in the ns sequencing data and the genplay multi-genome software to assign all snp-containing reads to the two parental chromosomes, arbitrarily termed p1 or p2, using the phasing information that we previously generated. […]

PMCID: 4221384
PMID: 25306110
DOI: 10.1038/nsmb.2903

[…] as the log2 odds ratio. isor also produces a bedgraph file for visualization purposes where the score is given as the log2 odds ratio. visualization of the bedgraph files was performed with the genplay program (http://genplay.einstein.yu.edu/wiki/index.php/web_start). all area-proportional venn diagrams were created with eulerape (http://www.eulerdiagrams.org/eulerape)., for metagene […]

PMCID: 4006724
PMID: 24787348
DOI: 10.1371/journal.pgen.1004319

[…] a variety of approaches to systematically detect the simulated ards. this resulted in the development of a highly efficient two-step method to detect ards. in the first step, the island finder of genplay is used to detect regions of differential timing in the smoothed profiles; in the second step, the statistical significance of the islands thus defined is assessed by performing chi-square […]

PMCID: 3669306
PMID: 23741343
DOI: 10.1371/journal.pone.0064571

[…] is, when at least one member of the trio was homozygous for the reference or alternate allele (). comparison of the two phased trios was then used to graph preliminary blocks of inheritance using genplay, a multi-purpose genome analyzer . genplay provided a graphical visualization of the location of all the crossing-overs and some of the genetically detectable errors (gde) present […]

PMCID: 3636266
PMID: 23633960
DOI: 10.1371/journal.pgen.1003417

[…] h1 occupancy and gene expression levels at a 10 kb region centered around transcription start sites (tsss) as well as a 10 kb region centered around transcription termination sites (ttss) using genplay software . such metagene analysis revealed that h1 signals were always lower than chromatin input control within these regions (ip-in<0) (), suggesting a general depletion of h1 at gene […]


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GenPlay institution(s)
Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
GenPlay funding source(s)
Grants C024405 and C024172 from NYSTEM

GenPlay review

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Anonymous user #1933

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Desktop
Great software

Similar to IGV but much faster and a lot more functions