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DESCRIPTION
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DESCRIPTION
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Package: AlpsNMR
Type: Package
Title: Automated spectraL Processing System for NMR
Version: 4.7.2
Date: 2024-08-10
Encoding: UTF-8
Authors@R: c(
person(given = "Ivan",
family = "Montoliu Roura",
email = "[email protected]",
role = c("aut")),
person(given = "Sergio",
family = "Oller Moreno",
email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-8994-1549")),
person(given = "Francisco",
family = "Madrid Gambin",
email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0001-9333-0014")),
person(given = "Luis",
family = "Fernandez",
email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0001-9790-6287")),
person(given = "Laura",
family = "López Sánchez",
role = c("ctb")),
person(given = "Héctor",
family = "Gracia Cabrera",
email = "[email protected]",
role = c("aut")),
person(given = "Santiago",
family = "Marco Colás",
email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0003-2663-2965")),
person(given = "Nestlé Institute of Health Sciences",
role = "cph"),
person(given = "Institute for Bioengineering of Catalonia",
role = "cph"),
person(given = "Miller",
family = "Jack",
email = "[email protected]",
role=c("ctb"),
comment = c(ORCID = "0000-0002-6258-1299", "Autophase wrapper, ASICS export"))
)
Description: Reads Bruker NMR data directories both zipped and unzipped.
It provides automated and efficient signal processing for untargeted
NMR metabolomics.
It is able to interpolate the samples, detect outliers, exclude regions,
normalize, detect peaks, align the spectra, integrate peaks, manage metadata and
visualize the spectra.
After spectra proccessing, it can apply multivariate analysis on extracted data.
Efficient plotting with 1-D data is also available.
Basic reading of 1D ACD/Labs exported JDX samples is also available.
License: MIT + file LICENSE
URL: https://sipss.github.io/AlpsNMR/, https://github.com/sipss/AlpsNMR
BugReports: https://github.com/sipss/AlpsNMR/issues
LazyData: FALSE
Depends: R (>= 4.2)
Imports:
utils,
generics,
graphics,
stats,
grDevices,
cli,
magrittr (>= 1.5),
dplyr (>= 1.1.0),
signal (>= 0.7-6),
rlang (>= 0.3.0.1),
scales (>= 1.2.0),
stringr (>= 1.3.1),
tibble(>= 1.3.4),
tidyr (>= 1.0.0),
tidyselect,
readxl (>= 1.1.0),
purrr (>= 0.2.5),
glue (>= 1.2.0),
reshape2 (>= 1.4.3),
mixOmics (>= 6.22.0),
matrixStats (>= 0.54.0),
fs (>= 1.2.6),
rmarkdown (>= 1.10),
speaq (>= 2.4.0),
htmltools (>= 0.3.6),
pcaPP (>= 1.9-73),
ggplot2 (>= 3.1.0),
baseline (>= 1.2-1),
vctrs (>= 0.3.0),
BiocParallel (>= 1.34.0)
Suggests:
ASICS,
BiocStyle,
ChemoSpec,
cowplot,
curl,
DT (>= 0.5),
GGally (>= 1.4.0),
ggrepel (>= 0.8.0),
gridExtra,
knitr,
NMRphasing,
plotly (>= 4.7.1),
progressr,
SummarizedExperiment,
S4Vectors,
testthat (>= 2.0.0),
writexl (>= 1.0),
zip (>= 2.0.4)
biocViews: Software, Preprocessing, Visualization, Classification,
Cheminformatics, Metabolomics, DataImport
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr