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High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets
High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, W...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809091/ https://www.ncbi.nlm.nih.gov/pubmed/29432475 http://dx.doi.org/10.1371/journal.pone.0192858 |
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author | Madanecki, Piotr Bałut, Magdalena Buckley, Patrick G. Ochocka, J. Renata Bartoszewski, Rafał Crossman, David K. Messiaen, Ludwine M. Piotrowski, Arkadiusz |
author_facet | Madanecki, Piotr Bałut, Magdalena Buckley, Patrick G. Ochocka, J. Renata Bartoszewski, Rafał Crossman, David K. Messiaen, Ludwine M. Piotrowski, Arkadiusz |
author_sort | Madanecki, Piotr |
collection | PubMed |
description | High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp). |
format | Online Article Text |
id | pubmed-5809091 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-58090912018-02-28 High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets Madanecki, Piotr Bałut, Magdalena Buckley, Patrick G. Ochocka, J. Renata Bartoszewski, Rafał Crossman, David K. Messiaen, Ludwine M. Piotrowski, Arkadiusz PLoS One Research Article High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp). Public Library of Science 2018-02-12 /pmc/articles/PMC5809091/ /pubmed/29432475 http://dx.doi.org/10.1371/journal.pone.0192858 Text en © 2018 Madanecki et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Madanecki, Piotr Bałut, Magdalena Buckley, Patrick G. Ochocka, J. Renata Bartoszewski, Rafał Crossman, David K. Messiaen, Ludwine M. Piotrowski, Arkadiusz High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets |
title | High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets |
title_full | High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets |
title_fullStr | High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets |
title_full_unstemmed | High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets |
title_short | High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets |
title_sort | high-throughput tabular data processor – platform independent graphical tool for processing large data sets |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809091/ https://www.ncbi.nlm.nih.gov/pubmed/29432475 http://dx.doi.org/10.1371/journal.pone.0192858 |
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