| Type: | Package |
| Title: | Data Sets for 'specmine' |
| Version: | 0.0.3 |
| Date: | 2026-07-03 |
| Depends: | R (≥ 4.0.0) |
| LazyData: | true |
| RoxygenNote: | 8.0.0 |
| Description: | Provides the data sets used to exemplify 'specmine'. These data sets were formerly distributed with 'specmine', but they exceed current CRAN policy for package size. |
| Encoding: | UTF-8 |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/PedroFontao/specmine.datasets |
| BugReports: | https://github.com/PedroFontao/specmine.datasets/issues |
| NeedsCompilation: | no |
| Packaged: | 2026-07-06 09:35:07 UTC; pedrofontao |
| Author: | Christopher Costa [aut], Marcelo Maraschin [aut], Miguel Rocha [aut], Pedro Fontão [aut, cre], Sara Cardoso [aut], Telma Afonso [aut], C. Beleites [cph], Jie Hao [cph], Bruno Pereira [aut] |
| Maintainer: | Pedro Fontão <pedrofontao812004@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2026-07-14 16:40:02 UTC |
Human cachexia data
Description
Cachexia is a complex metabolic syndrome associated with an underlying illness (such as cancer) and characterized by loss of muscle with or without loss of fat mass (Evans et al., 2008). A total of 77 urine samples were collected, with 47 from patients with cachexia and 30 from control patients.
Usage
cachexia
Format
An object of class "list"
Source
Data originally made available through MetaboAnalyst.
References
Eisner et al. (2010) Learning to predict cancer-associated skeletal muscle wasting from 1h-nmr profiles of urinary metabolites. Metabolomics 7:25-34.
Cassava postharvest physiological deterioration
Description
Cassava is a root widely cultivated in tropical and subtropical regions for its starchy tuberous root, which is an important source of carbohydrates. It has a wide variety of applications, including animal feeding, culinary uses and alcoholic beverages. In some countries, cassava has also been tested as an ethanol biofuel feedstock.
Usage
cassavaPPD
Format
An object of class "list"
References
Uarrota et al. (2014) Metabolomics combined with chemometric tools (pca, hca, pls-da and svm) for screening cassava (manihot esculenta crantz) roots during postharvest physiological deterioration. Food Chemistry 161:67-78.
Brazilian propolis from different harvest seasons and agroecological regions (dataset)
Description
Propolis, or bee glue, is a sticky dark-colored substance produced from collected buds or plant exudates (resin) by bees (Apis mellifera L.). The resin is masticated, salivary enzymes are added, and the partially digested material is mixed with beeswax and used in the hive to seal walls, strengthen comb borders and embalm dead invaders (Wollenweber et al., 1990). The propolis samples are from NMR data and were collected in autumn (AU), winter (WI), spring (SP) and summer (SM) of 2010 from Apis mellifera hives located in southern Brazil (Santa Catarina State). A total of 59 samples were collected, distributed by season as follows: SM - 16 samples, AU and SP - 15 samples each, and WI - 13 samples. Three agroecological regions were defined for the different apiaries and distributed as follows: Highlands - 12 samples, Plain - 11 samples and Plateau - 36 samples.
Usage
propolis
Format
An object of class "list"
References
E. Wollenweber, B. M. Hausen, and W. Greenaway. Phenolic constituents and sensitizing properties of propolis, poplar balsam and balsam of Peru. Bulletin de Groupe Polyphenol, 15:112-120, 1990.
M. Maraschin, A. Somensi-Zeggio, S. K. Oliveira, S. Kuhnen, M. M. Tomazzoli, A. C. M. Zeri, R. Carreira, and M. Rocha. A machine learning and chemometrics assisted interpretation of spectroscopic data - a NMR-based metabolomics platform for the assessment of Brazilian propolis. 2012.
Brazilian propolis from different harvest seasons and agroecological regions (sample list)
Description
Propolis, or bee glue, is a sticky dark-colored substance produced from collected buds or plant exudates (resin) by bees (Apis mellifera L.). The resin is masticated, salivary enzymes are added, and the partially digested material is mixed with beeswax and used in the hive to seal walls, strengthen comb borders and embalm dead invaders (Wollenweber et al., 1990). The propolis samples are from NMR data and were collected in autumn (AU), winter (WI), spring (SP) and summer (SM) of 2010 from Apis mellifera hives located in southern Brazil (Santa Catarina State). A total of 59 samples were collected, distributed by season as follows: SM - 16 samples, AU and SP - 15 samples each, and WI - 13 samples. Three agroecological regions were defined for the different apiaries and distributed as follows: Highlands - 12 samples, Plain - 11 samples and Plateau - 36 samples.
Usage
propolisSampleList
Format
An object of class "list"
References
E. Wollenweber, B. M. Hausen, and W. Greenaway. Phenolic constituents and sensitizing properties of propolis, poplar balsam and balsam of Peru. Bulletin de Groupe Polyphenol, 15:112-120, 1990.
M. Maraschin, A. Somensi-Zeggio, S. K. Oliveira, S. Kuhnen, M. M. Tomazzoli, A. C. M. Zeri, R. Carreira, and M. Rocha. A machine learning and chemometrics assisted interpretation of spectroscopic data - a NMR-based metabolomics platform for the assessment of Brazilian propolis. 2012.
Information on the library of NMR reference spectra in the specmine package
Description
This dataset provides information on the library of NMR spectra used as references in NMR metabolite identification.
Usage
spectra_options
Format
A data frame with 1816 observations on the following 9 variables. Each observation corresponds to a spectrum in the library.
SPCMNSA character vector with the spectra IDs.
SPCMNMA character vector with the metabolite IDs of the corresponding spectra.
FREQUENCYA character vector with the frequencies at which the spectra were obtained.
NUCLEUSA character vector indicating the examined nucleus. All observations are '1H'.
PHA character vector with the pH of the samples from which the spectra were obtained. May contain missing values.
TEMPERATUREA character vector with the temperature at which the spectra were obtained. May contain missing values.
SOLVENTA character vector with the solvent of the samples from which the spectra were obtained.
ORIGINAL_DATABASE_IDWhenever available, a character vector with the ID of the corresponding spectrum from the database where it was originally acquired.
DATABASEA character vector specifying the database from which the spectra were taken.
References
The spectra were taken from the HMDB, BMRB and SDBS databases.
Some spectra were internally acquired and are mentioned as OUR in the
DATABASE variable.
Mouse spinal cord LC-MS data
Description
This dataset consists of 12 LC-MS spectra samples in netCDF format from mouse spinal cord, divided into two groups: wild type and knockout. The data was obtained from MetaboAnalyst and originates from a study describing a general strategy for identifying endogenous substrates of enzymes by untargeted LC-MS analysis of tissue metabolomes from wild-type and enzyme-inactivated organisms.
Usage
spinalCord
Format
An object of class "list"
References
A. Saghatelian, S.A. Trauger, E.J. Want, E.G. Hawkins, G. Siuzdak, and B.F. Cravatt. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry, 43:14332-14339, 2004.