Vertical and horizontal integration of multi-omics data with miodin
Abstract Background Studies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is widely recognized that integrative omics analysis holds the promise to unl...
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| Format: | Article |
| Language: | English |
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BMC
2019-12-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-019-3224-4 |
| _version_ | 1818623562711302144 |
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| author | Benjamin Ulfenborg |
| author_facet | Benjamin Ulfenborg |
| author_sort | Benjamin Ulfenborg |
| collection | DOAJ |
| description | Abstract Background Studies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is widely recognized that integrative omics analysis holds the promise to unlock novel and actionable biological insights into health and disease. Integration of multi-omics data remains challenging, however, and requires combination of several software tools and extensive technical expertise to account for the properties of heterogeneous data. Results This paper presents the miodin R package, which provides a streamlined workflow-based syntax for multi-omics data analysis. The package allows users to perform analysis of omics data either across experiments on the same samples (vertical integration), or across studies on the same variables (horizontal integration). Workflows have been designed to promote transparent data analysis and reduce the technical expertise required to perform low-level data import and processing. Conclusions The miodin package is implemented in R and is freely available for use and extension under the GPL-3 license. Package source, reference documentation and user manual are available at https://gitlab.com/algoromics/miodin. |
| first_indexed | 2024-12-16T18:43:02Z |
| format | Article |
| id | doaj.art-9d990ae60bbd4222a8925a176bcd68b3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-16T18:43:02Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9d990ae60bbd4222a8925a176bcd68b32022-12-21T22:20:58ZengBMCBMC Bioinformatics1471-21052019-12-0120111010.1186/s12859-019-3224-4Vertical and horizontal integration of multi-omics data with miodinBenjamin Ulfenborg0School of Bioscience, University of SkövdeAbstract Background Studies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is widely recognized that integrative omics analysis holds the promise to unlock novel and actionable biological insights into health and disease. Integration of multi-omics data remains challenging, however, and requires combination of several software tools and extensive technical expertise to account for the properties of heterogeneous data. Results This paper presents the miodin R package, which provides a streamlined workflow-based syntax for multi-omics data analysis. The package allows users to perform analysis of omics data either across experiments on the same samples (vertical integration), or across studies on the same variables (horizontal integration). Workflows have been designed to promote transparent data analysis and reduce the technical expertise required to perform low-level data import and processing. Conclusions The miodin package is implemented in R and is freely available for use and extension under the GPL-3 license. Package source, reference documentation and user manual are available at https://gitlab.com/algoromics/miodin.https://doi.org/10.1186/s12859-019-3224-4Multi-omicsData analysisData integrationTransparency |
| spellingShingle | Benjamin Ulfenborg Vertical and horizontal integration of multi-omics data with miodin BMC Bioinformatics Multi-omics Data analysis Data integration Transparency |
| title | Vertical and horizontal integration of multi-omics data with miodin |
| title_full | Vertical and horizontal integration of multi-omics data with miodin |
| title_fullStr | Vertical and horizontal integration of multi-omics data with miodin |
| title_full_unstemmed | Vertical and horizontal integration of multi-omics data with miodin |
| title_short | Vertical and horizontal integration of multi-omics data with miodin |
| title_sort | vertical and horizontal integration of multi omics data with miodin |
| topic | Multi-omics Data analysis Data integration Transparency |
| url | https://doi.org/10.1186/s12859-019-3224-4 |
| work_keys_str_mv | AT benjaminulfenborg verticalandhorizontalintegrationofmultiomicsdatawithmiodin |