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Title:
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data | BMC Bioinformatics
Description:
Background Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from āgenomic interactionā studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. Results This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite āpgltoolsā: a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Conclusions Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.
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Keywords {š}
pgl, file, data, entries, pgltools, genomic, files, locus, interaction, pairedgenomicloci, operation, article, overlap, analysis, tool, chromatin, entry, genome, operations, suite, loci, standard, pubmed, format, single, formats, bioinformatics, manipulation, hic, python, bed, overlapping, arithmetic, interactions, open, number, shown, returns, google, scholar, software, access, analyses, pypy, efficient, bedtools, matrix, visualization, kaf, information,
Topics {āļø}
manipulating paired-genomic-loci data paired-genomic-loci data generated paired-genomic-loci file standard paired-genomic-loci data paired-genomic-lociĀ data paired-genomic-loci data [3 generating pre-published data article download pdf overlapping paired-genomic-loci paired-genomic-loci analyses multiple paired-genomic-loci storing paired-genomic-loci paired-end tag sequencing gene expression triplet sparse matrix ļæ½genomic interactionā studies paired-genomic-loci software tool suite chia-pet tool related subjects analysis tool suite ļæ½genomic interactionā data genomic interaction data 3d conformation differential coverage depth privacy choices/manage cookies chromatin interaction data peak calling algorithms paired-loci comprising genomic arithmetic pipeline genomic interaction field creative commons license full access locus chromatin state genomic-interactions data 5c data analysis chromatin architecture reorganization coverage operation returns suitable storage formats enable efficient annotation iterative bioinformatics analyses desired genomic region efficiently finds consecutive depth flow chart analyzing loop-resolution checked multiple times data type resulting european economic area berkum nl van antosiewicz-bourget je
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headline:Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data
description:Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from āgenomic interactionā studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite āpgltoolsā: a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at
www.github.com/billgreenwald/pgltools
, and a python module of the operations can be installed from PyPI via the PyGLtools module.
datePublished:2017-04-07T00:00:00Z
dateModified:2017-04-07T00:00:00Z
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license:http://creativecommons.org/publicdomain/zero/1.0/
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keywords:
Hi-CChIA-PET
Chromatin conformation capture
Peak
Paired-genomic-loci
Tool suite
Bedtools
Genomic arithmetic
Bioinformatics
Microarrays
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Algorithms
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headline:Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data
description:Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from āgenomic interactionā studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite āpgltoolsā: a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at
www.github.com/billgreenwald/pgltools
, and a python module of the operations can be installed from PyPI via the PyGLtools module.
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dateModified:2017-04-07T00:00:00Z
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Hi-CChIA-PET
Chromatin conformation capture
Peak
Paired-genomic-loci
Tool suite
Bedtools
Genomic arithmetic
Bioinformatics
Microarrays
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Algorithms
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