DRomics (Q79666): Difference between revisions
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Property / last update: 24 January 2023 / rank | |||||||||||||||
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Property / author: Marie-Laure Laure Delignette-Muller / rank | |||||||||||||||
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Property / author: Aurélie Siberchicot / rank | |||||||||||||||
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Property / maintained by: Aurelie Siberchicot / rank | |||||||||||||||
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Property / copyright license: GNU General Public License, version 2.0 / rank | |||||||||||||||
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Property / cites work: DRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment / rank | |||||||||||||||
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publication date: 16 January 2019
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publication date: 16 September 2019
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publication date: 22 September 2020
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publication date: 23 September 2020
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publication date: 9 February 2021
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publication date: 4 October 2021
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publication date: 6 January 2022
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publication date: 31 January 2024
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31 January 2024
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Property / last update: 31 January 2024 / rank | |||||||||||||||
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Property / maintained by: Aurelie Siberchicot / rank | |||||||||||||||
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Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) <doi:10.24072/pcjournal.325> and Larras et al (2018) <doi:10.1021/acs.est.8b04752>. | |||||||||||||||
Property / description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) <doi:10.24072/pcjournal.325> and Larras et al (2018) <doi:10.1021/acs.est.8b04752>. / rank | |||||||||||||||
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Property / author: Marie-Laure Laure Delignette-Muller / rank | |||||||||||||||
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Property / author: Elise Billoir / rank | |||||||||||||||
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Property / author: Aurélie Siberchicot / rank | |||||||||||||||
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Property / copyright license: GNU General Public License, version 2.0 / rank | |||||||||||||||
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Property / copyright license: GNU General Public License, version 3.0 / rank | |||||||||||||||
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edition/version: expanded from: GPL (≥ 2) (English) | |||||||||||||||
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Property / depends on software: DESeq2 / rank | |||||||||||||||
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Property / depends on software: SummarizedExperiment / rank | |||||||||||||||
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software version identifier: ≥ 3.5.0 | |||||||||||||||
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Property / cites work: DRomics, a workflow to exploit dose-response omics data in ecotoxicology / rank | |||||||||||||||
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Property / cites work: DRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment / rank | |||||||||||||||
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Latest revision as of 19:56, 12 March 2024
Dose Response for Omics
Language | Label | Description | Also known as |
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English | DRomics |
Dose Response for Omics |
Statements
31 January 2024
0 references
Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) <doi:10.24072/pcjournal.325> and Larras et al (2018) <doi:10.1021/acs.est.8b04752>.
0 references
expanded from: GPL (≥ 2) (English)
0 references