odbc - Connect to ODBC Compatible Databases (using the DBI Interface)

A DBI-compatible interface to ODBC databases.

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unixodbccpp

13.11 score 30 dependents 3.5k scripts 156k downloads

MassSpecWavelet - Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.

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immunooncologymassspectrometryproteomicspeakdetection

9.57 score 11 stars 21 dependents 47 scripts 4.0k downloads

MassSpecWavelet - Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.

Last updated

immunooncologymassspectrometryproteomicspeakdetection

7.63 score 11 stars 21 dependents 44 scripts

AlpsNMR - Automated spectraL Processing System for NMR

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.

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softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport

7.54 score 16 stars 1 dependents 15 scripts 536 downloads

AlpsNMR - Automated spectraL Processing System for NMR

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.

Last updated

softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport

7.17 score 17 stars 1 dependents 12 scripts

condformat - Conditional Formatting in Data Frames

Apply and visualize conditional formatting to data frames in R. It renders a data frame with cells formatted according to criteria defined by rules, using a tidy evaluation syntax. The table is printed either opening a web browser or within the 'RStudio' viewer if available. The conditional formatting rules allow to highlight cells matching a condition or add a gradient background to a given column. This package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and exporting to an 'xlsx' file.

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formattinghtmllatextablevisualisation

6.57 score 25 stars 1 dependents 98 scripts 803 downloads

GCIMS - Pre-processing for GC-IMS data

A package for the analysis of ion mobility spectrometry (IMS) measurements, as well as samples from multicapillary columns coupled with IMS (MCC-IMS) and gas chromatography coupled to ion mobility spectrometry (GC-IMS). The package provides a complete workflow for the analysis, importing the data, preprocessing the spectra as well as classification and regression techniques for the modelling of the spectra. The package also includes visualization helpers, to represent topographic plots, extracted and total ion chromatograms and IMS spectra.

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softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport

4.56 score 4 stars 9 scripts

sgolay - Efficient Savitzky-Golay Filtering

Smoothing signals and computing their derivatives is a common requirement in signal processing workflows. Savitzky-Golay filters are a established method able to do both (Savitzky and Golay, 1964 <doi:10.1021/ac60214a047>). This package implements one dimensional Savitzky-Golay filters that can be applied to vectors and matrices (either row-wise or column-wise). Vectorization and memory allocations have been profiled to reduce computational fingerprint. Short filter lengths are implemented in the direct space, while longer filters are implemented in frequency space, using a Fast Fourier Transform (FFT).

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openblas

3.54 score 7 stars 2 scripts 186 downloads

ChemometricsWithR - Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences (2nd Edition)

Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences", 2nd edition, by Ron Wehrens, Springer (2019).

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3.18 score 18 stars 17 scripts 22 downloads