Showing 96 of total 96 results (show query)
bioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 4 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
22.1 match 196 stars 14.31 score 984 scripts 11 dependentsbioc
TargetSearch:A package for the analysis of GC-MS metabolite profiling data
This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.
Maintained by Alvaro Cuadros-Inostroza. Last updated 4 months ago.
massspectrometrypreprocessingdecisiontreeimmunooncologybiocbioconductorgc-msmass-spectrometry
20.4 match 4 stars 7.42 score 3 scripts
agrocares
OBIC:Calculate the Open Bodem Index (OBI) Score
The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices. The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI. More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Maintained by Sven Verweij. Last updated 6 months ago.
18.0 match 11 stars 6.82 score 20 scripts
arsilva87
soilphysics:Soil Physical Analysis
Basic and model-based soil physical analyses.
Maintained by Anderson Rodrigo da Silva. Last updated 3 years ago.
18.1 match 11 stars 4.83 score 12 scripts
spang-lab
FastRet:Retention Time Prediction in Liquid Chromatography
A framework for predicting retention times in liquid chromatography. Users can train custom models for specific chromatography columns, predict retention times using existing models, or adjust existing models to account for altered experimental conditions. The provided functionalities can be accessed either via the R console or via a graphical user interface. Related work: Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>.
Maintained by Tobias Schmidt. Last updated 1 months ago.
retentiontimechromotographylc-msdata-sciencelcmsopenjdk
23.9 match 3.48 score 4 scripts
cbielow
PTXQC:Quality Report Generation for MaxQuant and mzTab Results
Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Maintained by Chris Bielow. Last updated 1 years ago.
drag-and-drophacktoberfestheatmapmatch-between-runsmaxquantmetricmztabopenmsproteomicsquality-controlquality-metricsreport
8.6 match 42 stars 9.35 score 105 scripts 1 dependents
yufree
pmd:Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
Maintained by Miao YU. Last updated 2 months ago.
mass-spectrometrymetabolomicsnon-target
12.0 match 10 stars 6.68 score 40 scriptsyufree
enviGCMS:GC/LC-MS Data Analysis for Environmental Science
Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Maintained by Miao YU. Last updated 2 months ago.
environmentmass-spectrometrymetabolomics
11.5 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
IntEREst:Intron-Exon Retention Estimator
This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).
Maintained by Ali Oghabian. Last updated 6 days ago.
softwarealternativesplicingcoveragedifferentialsplicingsequencingrnaseqalignmentnormalizationdifferentialexpressionimmunooncology
17.2 match 4.16 score 12 scripts
wkumler
RaMS:R Access to Mass-Spec Data
R-based access to mass-spectrometry (MS) data. While many packages exist to process MS data, many of these make it difficult to access the underlying mass-to-charge ratio (m/z), intensity, and retention time of the files themselves. This package is designed to format MS data in a tidy fashion and allows the user perform the plotting and analysis.
Maintained by William Kumler. Last updated 5 months ago.
mass-spectrometry-datatidy-data
7.5 match 24 stars 8.78 score 84 scripts 5 dependentsbioc
IPO:Automated Optimization of XCMS Data Processing parameters
The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.
Maintained by Thomas Lieb. Last updated 5 months ago.
immunooncologymetabolomicsmassspectrometry
7.0 match 34 stars 8.14 score 41 scripts
sriharitn
foretell:Projecting Customer Retention Based on Fader and Hardie Probability Models
Project Customer Retention based on Beta Geometric, Beta Discrete Weibull and Latent Class Discrete Weibull Models.This package is based on Fader and Hardie (2007) <doi:10.1002/dir.20074> and Fader and Hardie et al. (2018) <doi:10.1016/j.intmar.2018.01.002>.
Maintained by Srihari Jaganathan. Last updated 2 months ago.
13.6 match 5 stars 3.70 score 2 scripts
ploner
RMixpanel:API for Mixpanel
Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention, funnel and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Maintained by Meinhard Ploner. Last updated 6 years ago.
analyticsmixpanelmixpanel-apitracking
11.3 match 18 stars 4.00 score 11 scripts
cpanse
protViz:Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Maintained by Christian Panse. Last updated 1 years ago.
funmass-spectrometrypeptide-identificationproteomicsquantificationvisualizationcpp
5.4 match 11 stars 7.88 score 72 scripts 2 dependentsbioc
MetaboCoreUtils:Core Utils for Metabolomics Data
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.
Maintained by Johannes Rainer. Last updated 5 months ago.
infrastructuremetabolomicsmassspectrometrymass-spectrometry
4.5 match 9 stars 9.40 score 58 scripts 36 dependents
alisonlanski
IPEDSuploadables:Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload
Starting from user-supplied institutional data, these scripts transform, aggregate, and reshape the information to produce key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System) through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes. Final files are saved locally to a location of the user's choice. User-friendly readable files can also be produced for purposes of data review and validation.
Maintained by Alison Lanski. Last updated 3 months ago.
5.7 match 8 stars 7.05 score 39 scripts
mottensmann
GCalignR:Simple Peak Alignment for Gas-Chromatography Data
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Maintained by Meinolf Ottensmann. Last updated 6 months ago.
6.1 match 5 stars 6.39 score 41 scriptsbioc
peakPantheR:Peak Picking and Annotation of High Resolution Experiments
An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.
Maintained by Arnaud Wolfer. Last updated 5 months ago.
massspectrometrymetabolomicspeakdetectionfeature-detectionmass-spectrometry
5.7 match 12 stars 6.82 score 23 scripts
framverse
framrsquared:FRAM Database Interface
A convenient tool for interfacing with FRAM access databases in R environments.
Maintained by Ty Garber. Last updated 3 months ago.
6.9 match 6 stars 5.06 score 9 scriptsbioc
adductomicsR:Processing of adductomic mass spectral datasets
Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.
Maintained by Josie Hayes. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui
8.6 match 1 stars 4.00 score 5 scripts
cran
HydroMe:Estimating Water Retention and Infiltration Model Parameters using Experimental Data
Contains functions for estimating the parameters of infiltration and water retention models using the curve-fitting methods as discussed in Omuto and Gumbe (2009) ("Estimating water infiltration and retention characteristics using a computer program in R"<doi:10.1016/j.cageo.2008.08.011>). The models considered are those that are commonly used in soil science. Version 2 of the package has new models for water retention characteristic curves.
Maintained by Christian Thine Omuto. Last updated 10 months ago.
32.7 match 1 stars 1.00 score
dusadrian
QCA:Qualitative Comparative Analysis
An extensive set of functions to perform Qualitative Comparative Analysis: crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA') and fuzzy sets ('fsQCA'), using a GUI - graphical user interface. 'QCA' is a methodology that bridges the qualitative and quantitative divide in social science research. It uses a Boolean minimization algorithm, resulting in a minimal causal configuration associated with a given phenomenon.
Maintained by Adrian Dusa. Last updated 1 months ago.
4.8 match 2 stars 6.78 score 110 scripts 4 dependents
mdsteiner
EFAtools:Fast and Flexible Implementations of Exploratory Factor Analysis Tools
Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Maintained by Markus Steiner. Last updated 3 months ago.
4.9 match 10 stars 6.57 score 83 scripts 1 dependents
klausvigo
phangorn:Phylogenetic Reconstruction and Analysis
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
Maintained by Klaus Schliep. Last updated 1 months ago.
softwaretechnologyqualitycontrolphylogenetic-analysisphylogeneticsopenblascpp
1.9 match 206 stars 16.69 score 2.5k scripts 135 dependentsbioc
metabCombiner:Method for Combining LC-MS Metabolomics Feature Measurements
This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.
Maintained by Hani Habra. Last updated 5 months ago.
softwaremassspectrometrymetabolomicsmass-spectrometry
5.5 match 10 stars 5.65 score 5 scripts
filzmoserp
chemometrics:Multivariate Statistical Analysis in Chemometrics
R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).
Maintained by Peter Filzmoser. Last updated 2 years ago.
4.0 match 4 stars 6.72 score 213 scripts 4 dependentsbioc
MsFeatures:Functionality for Mass Spectrometry Features
The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.
Maintained by Johannes Rainer. Last updated 5 months ago.
infrastructuremassspectrometrymetabolomics
3.5 match 7 stars 7.70 score 32 scripts 12 dependents
paulojus
geoR:Analysis of Geostatistical Data
Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.
3.5 match 10 stars 7.57 score 1.8k scripts 12 dependentsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 4 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
2.0 match 130 stars 12.81 score 772 scripts 36 dependentsbioc
specL:specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>.
Maintained by Christian Panse. Last updated 5 months ago.
massspectrometryproteomicsddadiamass-spectrometry
4.7 match 1 stars 5.46 score 12 scripts
ethanbass
chromatographR:Chromatographic Data Analysis Toolset
Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.
Maintained by Ethan Bass. Last updated 2 days ago.
bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research
4.0 match 18 stars 6.36 score 8 scripts 1 dependentscran
CADF:Customer Analytics Data Formatting
Converts customer transaction data (ID, purchase date) into a R6 class called customer. The class stores various customer analytics calculations at the customer level. The package also contains functionality to convert data in the R6 class to data.frames that can serve as inputs for various customer analytics models.
Maintained by Ludwig Steven. Last updated 5 months ago.
12.6 match 2.00 scorebioc
flagme:Analysis of Metabolomics GC/MS Data
Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.
Maintained by Mark Robinson. Last updated 5 months ago.
differentialexpressionmassspectrometry
5.4 match 4.30 score 2 scripts
bioxgeo
geodiv:Methods for Calculating Gradient Surface Metrics
Methods for calculating gradient surface metrics for continuous analysis of landscape features.
Maintained by Annie C. Smith. Last updated 1 years ago.
3.8 match 11 stars 5.88 score 23 scripts 1 dependentsbioc
hdxmsqc:An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.
Maintained by Oliver M. Crook. Last updated 5 months ago.
qualitycontroldataimportproteomicsmassspectrometrymetabolomics
5.1 match 4.30 score 2 scriptsbioc
MsQuality:MsQuality - Quality metric calculation from Spectra and MsExperiment objects
The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.
Maintained by Thomas Naake. Last updated 2 months ago.
metabolomicsproteomicsmassspectrometryqualitycontrolmass-spectrometryqc
4.0 match 7 stars 5.45 score 2 scriptsethanbass
mzinspectr:Read and Analyze Mass Spectrometry Alignment Files
A few functions for analyzing MS-DIAL alignments in R. Includes functions for feature normalization, subtraction of blanks, and mass library (msp) search.
Maintained by Ethan Bass. Last updated 5 months ago.
cheminformaticsgc-mslc-msmetabolomics
7.8 match 3 stars 2.78 scorebioc
MsCoreUtils:Core Utils for Mass Spectrometry Data
MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 6 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils
2.0 match 16 stars 10.52 score 41 scripts 71 dependents
idslme
IDSL.IPA:Intrinsic Peak Analysis (IPA) for HRMS Data
A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
Maintained by Dinesh Barupal. Last updated 2 years ago.
exposomefeature-detectionlipidomicsmass-spectrometrymetabolomicspeak-detectionpeak-pickingsmall-moleculeuntargeted-metabolomics
4.3 match 13 stars 4.89 score 1 scripts 4 dependents
nanxstats
enpls:Ensemble Partial Least Squares Regression
An algorithmic framework for measuring feature importance, outlier detection, model applicability domain evaluation, and ensemble predictive modeling with (sparse) partial least squares regressions.
Maintained by Nan Xiao. Last updated 3 years ago.
chemometricsdimensionality-reductionensemble-learningmachine-learningoutlier-detectionpartial-least-squares-regression
3.8 match 18 stars 5.56 score 40 scripts
calfarog
GREENeR:Geospatial Regression Equation for European Nutrient Losses (GREEN)
Tools and methods to apply the model Geospatial Regression Equation for European Nutrient losses (GREEN); Grizzetti et al. (2005) <doi:10.1016/j.jhydrol.2004.07.036>; Grizzetti et al. (2008); Grizzetti et al. (2012) <doi:10.1111/j.1365-2486.2011.02576.x>; Grizzetti et al. (2021) <doi:10.1016/j.gloenvcha.2021.102281>.
Maintained by C. Alfaro. Last updated 7 months ago.
calibrationgeospatialnutrientplots
5.0 match 1 stars 4.00 score 9 scripts
ncss-tech
soilDB:Soil Database Interface
A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Maintained by Andrew Brown. Last updated 8 days ago.
ksslnasisnrcssoilsoil-data-accesssoil-surveysoilwebsqlusda
1.8 match 87 stars 11.34 score 1.0k scripts 1 dependentsbioc
MetaboAnnotation:Utilities for Annotation of Metabolomics Data
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
Maintained by Johannes Rainer. Last updated 3 months ago.
infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry
2.8 match 15 stars 6.98 score 35 scripts
tverbeke
SMCRM:Data Sets for Statistical Methods in Customer Relationship Management by Kumar and Petersen (2012).
Data Sets for Kumar and Petersen (2012). Statistical Methods in Customer Relationship Management, Wiley: New York.
Maintained by Tobias Verbeke. Last updated 12 years ago.
14.0 match 1.38 score 24 scripts
ropensci
webchem:Chemical Information from the Web
Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Maintained by Tamás Stirling. Last updated 3 months ago.
cas-numberchemical-informationchemspideridentifierropensciwebscraping
1.9 match 165 stars 10.31 score 173 scripts 10 dependents
aariq
chemhelper:Helper Functions For Dealing With GCMS and LCMS data from IonAnalytics
Provides helper functions for parsing data exported from IonAnalytics, calculating retention indecies, and other miscelanous helper functions to assist in data wrangling.
Maintained by Eric Scott. Last updated 2 years ago.
analytical-chemistrymultivariate-analysispls
7.5 match 4 stars 2.41 score 13 scripts
okdll
flowTraceR:Tracing Information Flow for Inter-Software Comparisons in Mass Spectrometry-Based Bottom-Up Proteomics
Useful functions to standardize software outputs from ProteomeDiscoverer, Spectronaut, DIA-NN and MaxQuant on precursor, modified peptide and proteingroup level and to trace software differences for identifications such as varying proteingroup denotations for common precursor.
Maintained by Oliver Kardell. Last updated 3 years ago.
3.1 match 3 stars 5.17 score 11 scripts 1 dependents
jpquast
protti:Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Maintained by Jan-Philipp Quast. Last updated 5 months ago.
data-analysislip-msmass-spectrometryomicsproteinproteomicssystems-biology
1.9 match 61 stars 8.58 score 83 scriptsbioc
IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.
geneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicingvisualizationstatisticalmethodtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologytranscriptomicsrnaseqannotationfunctionalpredictiongenepredictiondataimportmultiplecomparisonbatcheffectimmunooncology
1.7 match 108 stars 9.26 score 125 scripts
ms609
TreeSearch:Phylogenetic Analysis with Discrete Character Data
Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.
Maintained by Martin R. Smith. Last updated 5 days ago.
bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-searchcpp
2.0 match 7 stars 7.89 score 51 scripts
keithmcnulty
peopleanalyticsdata:Data Sets for Keith McNulty's Handbook of Regression Modeling in People Analytics
Data sets for statistical inference modeling related to People Analytics. Contains various data sets from the book 'Handbook of Regression Modeling in People Analytics' by Keith McNulty (2020).
Maintained by Keith McNulty. Last updated 4 years ago.
4.0 match 6 stars 3.71 score 17 scripts
rcapell
HYPEtools:Tools for Processing and Analyzing Files from the Hydrological Catchment Model HYPE
Work with model files (setup, input, output) from the hydrological catchment model HYPE: Streamlined file import and export, standard evaluation plot routines, diverse post-processing and aggregation routines for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955> and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.
Maintained by Rene Capell. Last updated 28 days ago.
1.9 match 17 stars 7.54 score 26 scriptsbioc
SpliceWiz:interactive analysis and visualization of alternative splicing in R
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
Maintained by Alex Chit Hei Wong. Last updated 6 days ago.
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
2.2 match 16 stars 6.41 score 8 scripts
elweiser
AlleleRetain:Allele Retention, Inbreeding, and Demography
Simulate the effect of management or demography on allele retention and inbreeding accumulation in bottlenecked populations of animals with overlapping generations.
Maintained by Emily Weiser. Last updated 7 years ago.
9.2 match 1.48 score 1 scriptsbioc
metaMS:MS-based metabolomics annotation pipeline
MS-based metabolomics data processing and compound annotation pipeline.
Maintained by Yann Guitton. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
1.8 match 15 stars 7.50 score 15 scripts
dmkaplan2000
ConnMatTools:Tools for Working with Connectivity Data
Collects several different methods for analyzing and working with connectivity data in R. Though primarily oriented towards marine larval dispersal, many of the methods are general and useful for terrestrial systems as well.
Maintained by David M. Kaplan. Last updated 5 years ago.
3.7 match 3.48 score 60 scripts
taxonomicallyinformedannotation
tima:Taxonomically Informed Metabolite Annotation
This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.
Maintained by Adriano Rutz. Last updated 8 days ago.
metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome
1.9 match 9 stars 6.55 score 32 scripts 2 dependentsbioc
NormalyzerDE:Evaluation of normalization methods and calculation of differential expression analysis statistics
NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.
Maintained by Jakob Willforss. Last updated 5 months ago.
normalizationmultiplecomparisonvisualizationbayesianproteomicsmetabolomicsdifferentialexpressionbioconductorbioinformaticslimma
1.6 match 22 stars 7.30 score 38 scripts 1 dependents
ecor
soilwater:Implementation of Parametric Formulas for Soil Water Retention or Conductivity Curve
It is a set of R implementations of parametric formulas of soil water retention or conductivity curve. At the moment, only Van Genuchten (for soil water retention curve) and Mualem (for hydraulic conductivity) were implemented. See reference (<http://en.wikipedia.org/wiki/ Water_retention_curve>).
Maintained by Emanuele Cordano. Last updated 8 years ago.
3.6 match 1 stars 3.11 score 26 scriptsbioc
artMS:Analytical R tools for Mass Spectrometry
artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.
Maintained by David Jimenez-Morales. Last updated 5 months ago.
proteomicsdifferentialexpressionbiomedicalinformaticssystemsbiologymassspectrometryannotationqualitycontrolgenesetenrichmentclusteringnormalizationimmunooncologymultiplecomparisonanalysisanalyticalap-msbioconductorbioinformaticsmass-spectrometryphosphoproteomicspost-translational-modificationquantitative-analysis
1.7 match 14 stars 6.41 score 13 scriptscran
erer:Empirical Research in Economics with R
Several functions, datasets, and sample codes related to empirical research in economics are included. They cover the marginal effects for binary or ordered choice models, static and dynamic Almost Ideal Demand System (AIDS) models, and a typical event analysis in finance.
Maintained by Changyou Sun. Last updated 6 months ago.
3.3 match 3 stars 3.34 score 211 scripts 1 dependents
casact
imaginator:Simulate General Insurance Policies and Losses
Simulate general insurance policies, losses and loss emergence. The package contemplates deterministic and stochastic policy retention and growth scenarios. Retention and growth rates are percentages relative to the expiring portfolio. Claims are simulated for each policy. This is accomplished either be assuming a frequency distribution per development lag or by generating random wait times until claim emergence and settlement. Loss simulation uses standard loss distributions for claim amounts.
Maintained by Brian Fannin. Last updated 3 years ago.
2.0 match 14 stars 5.51 score 23 scriptsbioc
BiocFHIR:Illustration of FHIR ingestion and transformation using R
FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.
Maintained by Vincent Carey. Last updated 5 months ago.
infrastructuredataimportdatarepresentationfhir
1.9 match 4 stars 5.78 score 15 scripts
kwb-r
keys.lid:R Package for Simulating the Impact of Different LIDs under Varying Climate Boundary Conditions on Annual Volume Rainfall Retention
R Package for Simulating the Impact of Different LIDs (Low Impact Development) under Varying Climate Boundary Conditions in China on annual VRR (Volume Rainfall Retention).
Maintained by Michael Rustler. Last updated 3 years ago.
bioretention-cellgreen-rooflidpermeable-pavementproject-keysrain-barrelswmm
3.2 match 1 stars 3.30 score 5 scriptsbioc
maser:Mapping Alternative Splicing Events to pRoteins
This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.
Maintained by Diogo F.T. Veiga. Last updated 5 months ago.
alternativesplicingtranscriptomicsvisualization
1.5 match 17 stars 6.74 score 18 scripts
maialba3
LipidMS:Lipid Annotation for LC-MS/MS DDA or DIA Data
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Maintained by M Isabel Alcoriza-Balaguer. Last updated 7 months ago.
1.9 match 2 stars 5.33 score 12 scripts 1 dependentsbioc
ncGTW:Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.
Maintained by Chiung-Ting Wu. Last updated 5 months ago.
softwaremassspectrometrymetabolomicsalignmentcpp
2.0 match 8 stars 4.90 score 3 scripts
blue-matter
openMSE:Easily Install and Load the 'openMSE' Packages
The 'openMSE' package is designed for building operating models, doing simulation modelling and management strategy evaluation for fisheries. 'openMSE' is an umbrella package for the 'MSEtool' (Management Strategy Evaluation toolkit), 'DLMtool' (Data-Limited Methods toolkit), and SAMtool (Stock Assessment Methods toolkit) packages. By loading and installing 'openMSE', users have access to the full functionality contained within these packages. Learn more about 'openMSE' at <https://openmse.com/>.
Maintained by Adrian Hordyk. Last updated 6 months ago.
1.7 match 14 stars 5.57 score 89 scriptsbioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
1.2 match 37 stars 7.81 score 29 scriptscran
mpwR:Standardized Comparison of Workflows in Mass Spectrometry-Based Bottom-Up Proteomics
Useful functions to analyze proteomic workflows including number of identifications, data completeness, missed cleavages, quantitative and retention time precision etc. Various software outputs are supported such as 'ProteomeDiscoverer', 'Spectronaut', 'DIA-NN' and 'MaxQuant'.
Maintained by Oliver Kardell. Last updated 1 years ago.
2.5 match 3.30 scorebioc
MetNet:Inferring metabolic networks from untargeted high-resolution mass spectrometry data
MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.
Maintained by Thomas Naake. Last updated 5 months ago.
immunooncologymetabolomicsmassspectrometrynetworkregression
1.7 match 4.70 score 1 scriptsbioc
MAIT:Statistical Analysis of Metabolomic Data
The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.
Maintained by Pol Sola-Santos. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicssoftware
1.7 match 4.60 score 20 scriptscran
MethodOpt:Advanced Method Optimization for Spectra-Generating Sampling and Analysis Instrumentation
A graphical user interface to apply an advanced method optimization algorithm to various sampling and analysis instruments. This includes generating experimental designs, uploading and viewing data, and performing various analyses to determine the optimal method. Details of the techniques used in this package are published in Gamble, Granger, & Mannion (2024) <doi:10.1021/acs.analchem.3c05763>.
Maintained by Stephanie Gamble. Last updated 6 months ago.
3.6 match 2.00 score
davisj95
YTAnalytics:Wrapper for 'YouTube Analytics' API
Simplify working with the 'YouTube Analytics' API <https://developers.google.com/youtube/analytics>. Collect data for your channel including geography, traffic sources, time period, etc.
Maintained by Jake Davis. Last updated 1 days ago.
2.0 match 3.48 scorecran
OrgMassSpecR:Organic Mass Spectrometry
Organic/biological mass spectrometry data analysis.
Maintained by Nathan Dodder. Last updated 8 years ago.
1.8 match 3.68 score 2 dependentsbioc
GeneStructureTools:Tools for spliced gene structure manipulation and analysis
GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.
Maintained by Beth Signal. Last updated 5 months ago.
immunooncologysoftwaredifferentialsplicingfunctionalpredictiontranscriptomicsalternativesplicingrnaseq
1.5 match 4.32 score 21 scripts
jacks306
minque:Various Linear Mixed Model Analyses
This package offers three important components: (1) to construct a use-defined linear mixed model, (2) to employ one of linear mixed model approaches: minimum norm quadratic unbiased estimation (MINQUE) (Rao, 1971) for variance component estimation and random effect prediction; and (3) to employ a jackknife resampling technique to conduct various statistical tests. In addition, this package provides the function for model or data evaluations.This R package offers fast computations for large data sets analyses for various irregular data structures.
Maintained by Jixiang Wu. Last updated 5 years ago.
3.6 match 1.75 score 28 scriptsbioc
MetCirc:Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.
Maintained by Thomas Naake. Last updated 5 months ago.
shinyappsmetabolomicsmassspectrometryvisualization
1.6 match 3.48 score 3 scriptscran
QCApro:Advanced Functionality for Performing and Evaluating Qualitative Comparative Analysis
Provides advanced functionality for performing configurational comparative research with Qualitative Comparative Analysis (QCA), including crisp-set, multi-value, and fuzzy-set QCA. It also offers advanced tools for sensitivity diagnostics and methodological evaluations of QCA.
Maintained by Alrik Thiem. Last updated 7 years ago.
4.8 match 1 stars 1.00 scorebioc
FRASER:Find RAre Splicing Events in RNA-Seq Data
Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.
Maintained by Christian Mertes. Last updated 5 months ago.
rnaseqalternativesplicingsequencingsoftwaregeneticscoverageaberrant-splicingdiagnosticsoutlier-detectionrare-diseaserna-seqsplicingopenblascpp
0.5 match 41 stars 8.50 score 155 scripts
cran
evidenceFactors:Reporting Tools for Sensitivity Analysis of Evidence Factors in Observational Studies
Provides tools for integrated sensitivity analysis of evidence factors in observational studies. When an observational study allows for multiple independent or nearly independent inferences which, if vulnerable, are vulnerable to different biases, we have multiple evidence factors. This package provides methods that respect type I error rate control. Examples are provided of integrated evidence factors analysis in a longitudinal study with continuous outcome and in a case-control study. Karmakar, B., French, B., and Small, D. S. (2019)<DOI:10.1093/biomet/asz003>.
Maintained by Bikram Karmakar. Last updated 5 years ago.
3.6 match 1.00 score 5 scriptsbioc
LOBSTAHS:Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.
Maintained by Henry Holm. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton
0.5 match 8 stars 6.56 score 9 scripts
jaehyunjoo
LCMSQA:Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment
The goal of 'LCMSQA' is to make it easy to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments using a 'shiny' application. This package provides interactive data visualizations for quality control (QC) samples, including total ion current chromatogram (TIC), base peak chromatogram (BPC), mass spectrum, extracted ion chromatogram (XIC), and feature detection results from internal standards or known metabolites.
Maintained by Jaehyun Joo. Last updated 1 years ago.
1.1 match 2.70 score 2 scripts
ivanp84
qtlc:Densitometric Analysis of Thin-Layer Chromatography Plates
Densitometric evaluation of the photo-archived quantitative thin-layer chromatography (TLC) plates.
Maintained by Ivan D. Pavicevic. Last updated 9 years ago.
2.0 match 1 stars 1.34 score 22 scripts
alexisdinno
paran:Horn's Test of Principal Components/Factors
An implementation of Horn's technique for numerically and graphically evaluating the components or factors retained in a principle components analysis (PCA) or common factor analysis (FA). Horn's method contrasts eigenvalues produced through a PCA or FA on a number of random data sets of uncorrelated variables with the same number of variables and observations as the experimental or observational data set to produce eigenvalues for components or factors that are adjusted for the sample error-induced inflation. Components with adjusted eigenvalues greater than one are retained. paran may also be used to conduct parallel analysis following Glorfeld's (1995) suggestions to reduce the likelihood of over-retention.
Maintained by Alexis Dinno. Last updated 11 months ago.
0.5 match 1 stars 4.09 score 86 scripts 2 dependents
r-ifpe
sistec:Tools to Analyze 'Sistec' Datasets
The Brazilian system for diploma registration and validation on technical and superior courses are managing by 'Sistec' platform, see <https://sistec.mec.gov.br/>. This package provides tools for Brazilian institutions to update the student's registration and make data analysis about their situation, retention and drop out.
Maintained by Samuel Macêdo. Last updated 4 years ago.
0.5 match 6 stars 3.52 score 11 scriptsecor
rasterList:A Raster Where Cells are Generic Objects
A S4 class has been created such that complex operations can be executed on each cell of a raster map. The raster of objects contains a raster map with the addition of a list of generic objects: one object for each raster cells. It allows to write few lines of R code for complex map algebra. Two environmental applications about frequency analysis of raster map of precipitation and creation of a raster map of soil water retention curves have been presented.
Maintained by Emanuele Cordano. Last updated 2 years ago.
climatehydrologyhydrology-statisticalhydrology-stormwater-analysis
0.5 match 1 stars 3.34 score 22 scripts
ullid
SoilHyP:Soil Hydraulic Properties
Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).
Maintained by Ullrich Dettmann. Last updated 2 years ago.
0.5 match 3.32 score 35 scripts 2 dependents
manuelperis
RpeakChrom:Tools for Chromatographic Column Characterization and Modelling Chromatographic Peak
The quantitative measurement and detection of molecules in HPLC should be carried out by an accurate description of chromatographic peaks. In this package non-linear fitting using a modified Gaussian model with a parabolic variance (PVMG) has been implemented to obtain the retention time and height at the peak maximum. This package also includes the traditional Van Deemter approach and two alternatives approaches to characterize chromatographic column.
Maintained by Manuel David Peris Diaz. Last updated 8 years ago.
0.5 match 1.00 score 4 scripts
singjc
RMSNumpress:'Rcpp' Bindings to Native C++ Implementation of MS Numpress
'Rcpp' bindings to the native C++ implementation of MS Numpress, that provides two compression schemes for numeric data from mass spectrometers. The library provides implementations of 3 different algorithms, 1 designed to compress first order smooth data like retention time or M/Z arrays, and 2 for compressing non smooth data with lower requirements on precision like ion count arrays. Refer to the publication (Teleman et al., (2014) <doi:10.1074/mcp.O114.037879>) for more details.
Maintained by Justin Sing. Last updated 4 years ago.
0.5 match 1.00 score 2 scripts