Showing 104 of total 104 results (show query)
fmmattioni
metabolic:Datasets and Functions for Reproducing Meta-Analyses
Dataset and functions from the meta-analysis published in Medicine & Science in Sports & Exercise. It contains all the data and functions to reproduce the analysis. "Effectiveness of HIIE versus MICT in Improving Cardiometabolic Risk Factors in Health and Disease: A Meta-analysis". Felipe Mattioni Maturana, Peter Martus, Stephan Zipfel, Andreas M Nieß (2020) <doi:10.1249/MSS.0000000000002506>.
Maintained by Felipe Mattioni Maturana. Last updated 1 years ago.
50.0 match 8 stars 3.60 score 8 scripts
bioc
BiGGR:Constraint based modeling in R using metabolic reconstruction databases
This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.
Maintained by Anand K. Gavai. Last updated 5 months ago.
systems biologypathwaynetworkgraphandnetworkvisualizationmetabolomics
32.4 match 4.67 score 58 scripts
yiluheihei
RevEcoR:Reverse Ecology Analysis on Microbiome
An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.
Maintained by Yang Cao. Last updated 6 years ago.
23.8 match 6 stars 5.77 score 22 scripts 1 dependentsbioc
gatom:Finding an Active Metabolic Module in Atom Transition Network
This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.
Maintained by Alexey Sergushichev. Last updated 5 months ago.
geneexpressiondifferentialexpressionpathwaysnetwork
22.1 match 6 stars 5.26 score 8 scriptsbioc
cosmosR:COSMOS (Causal Oriented Search of Multi-Omic Space)
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.
Maintained by Attila Gabor. Last updated 5 months ago.
cellbiologypathwaysnetworkproteomicsmetabolomicstranscriptomicsgenesignalingdata-integrationmetabolomic-datanetwork-modellingphosphoproteomics
15.8 match 59 stars 7.22 score 35 scripts
fawda123
EBASE:Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism
Estimate ecosystem metabolism in a Bayesian framework for individual water quality monitoring stations with continuous dissolved oxygen time series. A mass balance equation is used that provides estimates of parameters for gross primary production, respiration, and gas exchange. Methods adapted from Grace et al. (2015) <doi:10.1002/lom3.10011> and Wanninkhof (2014) <doi:10.4319/lom.2014.12.351>. Details in Beck et al. (2024) <doi:10.1002/lom3.10620>.
Maintained by Marcus Beck. Last updated 6 months ago.
20.2 match 4.91 score 18 scriptsfawda123
WtRegDO:Implement Weighted Regression on Dissolved Oxygen Time Series
A sample dataset and functions to implement weighted regression on dissolved oxygen time series are included as a simple example to reduce the effects of tidal advection. Functions are also available to estimate net ecosystem metabolism using the open-water method.
Maintained by Marcus W. Beck. Last updated 9 months ago.
detidingmetabolismweighted-regression
27.9 match 5 stars 3.50 score 42 scripts
gleon
LakeMetabolizer:Tools for the Analysis of Ecosystem Metabolism
A collection of tools for the calculation of freewater metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models).
Maintained by Jake Zwart. Last updated 2 years ago.
14.8 match 18 stars 5.94 score 122 scripts
pharmaverse
pharmaversesdtm:SDTM Test Data for the 'Pharmaverse' Family of Packages
A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. SDTM dataset specifications are described in the CDISC SDTM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.
Maintained by Edoardo Mancini. Last updated 12 hours ago.
11.8 match 15 stars 7.46 score 143 scripts
oyshilin
Sysrecon:Systematical Metabolic Reconstruction
In the past decade, genome-scale metabolic reconstructions have widely been used to comprehend the systems biology of metabolic pathways within an organism. Different GSMs are constructed using various techniques that require distinct steps, but the input data, information conversion and software tools are neither concisely defined nor mathematically or programmatically formulated in a context-specific manner.The tool that quantitatively and qualitatively specifies each reconstruction steps and can generate a template list of reconstruction steps dynamically selected from a reconstruction step reservoir, constructed based on all available published papers.
Maintained by Shilin Ouyang. Last updated 2 years ago.
27.8 match 2.70 score 1 scripts
jranke
mkin:Kinetic Evaluation of Chemical Degradation Data
Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using automatically generated C functions. Non-constant errors can be taken into account using variance by variable or two-component error models <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Maintained by Johannes Ranke. Last updated 1 months ago.
degradationfocus-kineticskinetic-modelskineticsodeode-model
8.4 match 11 stars 8.18 score 78 scripts 1 dependents
bioc
Macarron:Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
Macarron is a workflow for the prioritization of potentially bioactive metabolites from metabolomics experiments. Prioritization integrates strengths of evidences of bioactivity such as covariation with a known metabolite, abundance relative to a known metabolite and association with an environmental or phenotypic indicator of bioactivity. Broadly, the workflow consists of stratified clustering of metabolic spectral features which co-vary in abundance in a condition, transfer of functional annotations, estimation of relative abundance and differential abundance analysis to identify associations between features and phenotype/condition.
Maintained by Sagun Maharjan. Last updated 5 months ago.
sequencingmetabolomicscoveragefunctionalpredictionclustering
14.8 match 4.41 score 13 scripts
bioc
NetPathMiner:NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.
Maintained by Ahmed Mohamed. Last updated 4 months ago.
graphandnetworkpathwaysnetworkclusteringclassificationlibsbmllibxml2openblascpp
9.7 match 9 stars 6.56 score 9 scripts
statmanrobin
Stat2Data:Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
Maintained by Robin Lock. Last updated 6 years ago.
11.5 match 5 stars 4.94 score 544 scriptsfawda123
SWMPr:Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Tools for retrieving, organizing, and analyzing environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <https://cdmo.baruch.sc.edu/>. These tools address common challenges associated with continuous time series data for environmental decision making.
Maintained by Marcus W. Beck. Last updated 1 months ago.
7.8 match 13 stars 7.05 score 143 scripts 1 dependentsbioc
MWASTools:MWASTools: an integrated pipeline to perform metabolome-wide association studies
MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.
Maintained by Andrea Rodriguez-Martinez. Last updated 5 months ago.
metabolomicslipidomicscheminformaticssystemsbiologyqualitycontrol
14.5 match 3.78 score 5 scripts 1 dependents
maxconway
fbar:An Extensible Approach to Flux Balance Analysis
A toolkit for Flux Balance Analysis and related metabolic modeling techniques. Functions are provided for: parsing models in tabular format, converting parsed metabolic models to input formats for common linear programming solvers, and evaluating and applying gene-protein-reaction mappings. In addition, there are wrappers to parse a model, select a solver, find the metabolic fluxes, and return the results applied to the original model. Compared to other packages in this field, this package puts a much heavier focus on providing reusable components that can be used in the design of new implementation of new techniques, in particular those that involve large parameter sweeps. For a background on the theory, see What is Flux Balance Analysis <doi:10.1038/nbt.1614>.
Maintained by Max Conway. Last updated 5 years ago.
9.3 match 9 stars 5.49 score 23 scripts
cmerow
meteR:Fitting and Plotting Tools for the Maximum Entropy Theory of Ecology (METE)
Fit and plot macroecological patterns predicted by the Maximum Entropy Theory of Ecology (METE).
Maintained by Cory Merow. Last updated 6 years ago.
8.5 match 11 stars 5.35 score 41 scripts
january3
tmod:Feature Set Enrichment Analysis for Metabolomics and Transcriptomics
Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis. See Zyla et al (2019) <doi:10.1093/bioinformatics/btz447>.
Maintained by January Weiner. Last updated 2 months ago.
6.5 match 3 stars 6.88 score 168 scripts 1 dependents
r-forge
deSolve:Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')
Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.
Maintained by Thomas Petzoldt. Last updated 1 years ago.
3.5 match 12.33 score 8.0k scripts 427 dependentsbioc
MetaPhOR:Metabolic Pathway Analysis of RNA
MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.
Maintained by Emily Isenhart. Last updated 5 months ago.
metabolomicsrnaseqpathwaysgeneexpressiondifferentialexpressionkeggsequencingmicroarray
9.4 match 4.00 score 1 scriptsbioc
MicrobiomeProfiler:An R/shiny package for microbiome functional enrichment analysis
This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.
Maintained by Guangchuang Yu. Last updated 5 months ago.
microbiomesoftwarevisualizationkegg
5.4 match 37 stars 6.79 score 22 scripts
trenchproject
TrenchR:Tools for Microclimate and Biophysical Ecology
Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>.
Maintained by Lauren Buckley. Last updated 1 years ago.
5.3 match 13 stars 6.89 score 43 scriptsbioc
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
7.7 match 4.70 score 1 scriptsbioc
MetaboSignal:MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.
Maintained by Andrea Rodriguez-Martinez. Last updated 5 months ago.
graphandnetworkgenesignalinggenetargetnetworkpathwayskeggreactomesoftware
7.0 match 4.90 score 8 scripts
ropensci
spiro:Manage Data from Cardiopulmonary Exercise Testing
Import, process, summarize and visualize raw data from metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
Maintained by Simon Nolte. Last updated 26 days ago.
5.2 match 13 stars 6.35 score 43 scripts
maialba3
FAMetA:Fatty Acid Metabolic Analysis
Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.
Maintained by Maribel Alcoriza-Balaguer. Last updated 1 years ago.
8.9 match 1 stars 3.70 score 2 scripts
padpadpadpad
rTPC:Fitting and Analysing Thermal Performance Curves
Helps to fit thermal performance curves (TPCs). 'rTPC' contains 26 model formulations previously used to fit TPCs and has helper functions to set sensible start parameters, upper and lower parameter limits and estimate parameters useful in downstream analyses, such as cardinal temperatures, maximum rate and optimum temperature. See Padfield et al. (2021) <doi:10.1111/2041-210X.13585>.
Maintained by Daniel Padfield. Last updated 25 days ago.
3.6 match 25 stars 9.07 score 267 scripts
bioc
graphite:GRAPH Interaction from pathway Topological Environment
Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.
Maintained by Gabriele Sales. Last updated 5 months ago.
pathwaysthirdpartyclientgraphandnetworknetworkreactomekeggmetabolomicsbioinformaticsmirrorpathway-analysis
3.1 match 7 stars 10.17 score 122 scripts 21 dependents
gormleyi
MetabolAnalyze:Probabilistic Latent Variable Models for Metabolomic Data
Fits probabilistic principal components analysis, probabilistic principal components and covariates analysis and mixtures of probabilistic principal components models to metabolomic spectral data.
Maintained by Claire Gormley. Last updated 6 years ago.
10.8 match 1 stars 2.69 score 18 scripts 1 dependentsbioc
AWFisher:An R package for fast computing for adaptively weighted fisher's method
Implementation of the adaptively weighted fisher's method, including fast p-value computing, variability index, and meta-pattern.
Maintained by Zhiguang Huo. Last updated 5 months ago.
5.9 match 5 stars 4.70 score 4 scripts
karlines
LIM:Linear Inverse Model Examples and Solution Methods
Functions that read and solve linear inverse problems (food web problems, linear programming problems). These problems find solutions to linear or quadratic functions: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(ai*xi) subject to equality constraints Ex=f and inequality constraints Gx>=h.
Maintained by Karline Soetaert. Last updated 1 years ago.
6.5 match 4.28 score 32 scripts 1 dependentsbioc
POMA:Tools for Omics Data Analysis
The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.
Maintained by Pol Castellano-Escuder. Last updated 4 months ago.
batcheffectclassificationclusteringdecisiontreedimensionreductionmultidimensionalscalingnormalizationpreprocessingprincipalcomponentregressionrnaseqsoftwarestatisticalmethodvisualizationbioconductorbioinformaticsdata-visualizationdimension-reductionexploratory-data-analysismachine-learningomics-data-integrationpipelinepre-processingstatistical-analysisuser-friendlyworkflow
3.4 match 11 stars 8.23 score 20 scripts 1 dependentskarlines
limSolve:Solving Linear Inverse Models
Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) subject to equality constraints Ex=f and/or inequality constraints Gx>=h, (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.
Maintained by Karline Soetaert. Last updated 1 years ago.
3.3 match 4 stars 7.85 score 158 scripts 52 dependentspadpadpadpad
nls.multstart:Robust Non-Linear Regression using AIC Scores
Non-linear least squares regression with the Levenberg-Marquardt algorithm using multiple starting values for increasing the chance that the minimum found is the global minimum.
Maintained by Daniel Padfield. Last updated 2 months ago.
3.6 match 18 stars 7.08 score 552 scripts 2 dependents
netcoupler
NetCoupler:Inference of Causal Links Between a Network and an External Variable
The 'NetCoupler' algorithm identifies potential direct effects of correlated, high-dimensional variables formed as a network with an external variable. The external variable may act as the dependent/response variable or as an independent/predictor variable to the network.
Maintained by Luke Johnston. Last updated 1 years ago.
5.1 match 6 stars 4.78 score 7 scriptsr-forge
Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 6.38 score 522 scripts
yufree
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
3.6 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
benchdamic:Benchmark of differential abundance methods on microbiome data
Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.
Maintained by Matteo Calgaro. Last updated 4 months ago.
metagenomicsmicrobiomedifferentialexpressionmultiplecomparisonnormalizationpreprocessingsoftwarebenchmarkdifferential-abundance-methods
4.0 match 6 stars 5.73 score 8 scripts
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 12 months ago.
4.5 match 143 stars 5.01 score 143 scripts
tylermoulton
rMR:Importing Data from Loligo Systems Software, Calculating Metabolic Rates and Critical Tensions
Analysis of oxygen consumption data generated by Loligo (R) Systems respirometry equipment. The package includes a function for loading data output by Loligo's 'AutoResp' software (get.witrox.data()), functions for calculating metabolic rates over user-specified time intervals, extracting critical points from data using broken stick regressions based on Yeager and Ultsch (<DOI:10.1086/physzool.62.4.30157935>), and easy functions for converting between different units of barometric pressure.
Maintained by Tyler L. Moulton. Last updated 7 years ago.
6.6 match 3.38 score 200 scripts 1 dependents
middleton-lab
abd:The Analysis of Biological Data
The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Maintained by Kevin M. Middleton. Last updated 11 months ago.
4.0 match 6 stars 5.53 score 182 scripts 1 dependentsr-forge
Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 5.70 score 191 scriptsbioc
metapone:Conducts pathway test of metabolomics data using a weighted permutation test
The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.
Maintained by Tianwei Yu. Last updated 5 months ago.
technologymassspectrometrymetabolomicspathways
5.0 match 4.00 score 9 scripts
sizespectrum
mizer:Dynamic Multi-Species Size Spectrum Modelling
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Maintained by Gustav Delius. Last updated 2 months ago.
ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp
2.0 match 38 stars 9.43 score 207 scripts
pydemull
activAnalyzer:A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical Behavior Data
A tool to analyse 'ActiGraph' accelerometer data and to implement the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement. All the configured inputs relevant for interpreting the results are recorded in the report. In addition to the existing 'R' packages that are fully integrated with the app, the app uses some functions from the 'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
Maintained by Pierre-Yves de Müllenheim. Last updated 6 months ago.
accelerometeractigraphappmonitorshiny
3.5 match 5 stars 5.18 score 8 scripts
danielquiroz97
RGCxGC:Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
Maintained by Cristian Quiroz-Moreno. Last updated 2 years ago.
chemphyschemometricsgcxgcmultiway-algorithmspreprocessing
3.5 match 7 stars 4.77 score 17 scriptsbioc
OmnipathR:OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Maintained by Denes Turei. Last updated 20 days ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
1.7 match 126 stars 9.90 score 226 scripts 2 dependents
jwiley
pscore:Standardizing Physiological Composite Risk Endpoints
Provides a number of functions to simplify and automate the scoring, comparison, and evaluation of different ways of creating composites of data. It is particularly aimed at facilitating the creation of physiological composites of metabolic syndrome symptom score (MetSSS) and allostatic load (AL). Provides a wrapper to calculate the MetSSS on new data using the Healthy Hearts formula.
Maintained by Joshua F. Wiley. Last updated 3 years ago.
3.5 match 2 stars 4.72 score 13 scripts
yulab-smu
MMINP:Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor
Implements a computational framework to predict microbial community-based metabolic profiles with 'O2PLS' model. It provides procedures of model training and prediction. Paired microbiome and metabolome data are needed for modeling, and the trained model can be applied to predict metabolites of analogous environments using new microbial feature abundances.
Maintained by Wenli Tang. Last updated 2 years ago.
metabolite-predictionmetabolitesmicrobes
3.4 match 13 stars 4.81 score 9 scripts
kim3-sudo
nsm3data:Datasets to Accompany Hollander, Wolfe, and Chicken NSM3
Designed to add datasets which are used in the Nonparametric Statistical Methods textbook, 3rd edition.
Maintained by Sejin Kim. Last updated 1 years ago.
6.0 match 2.70 score 1 scripts
interstellar-consultation-services
covid19dbcand:Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R Format
Provides different datasets parsed from 'Drugbank' <https://www.drugbank.ca/covid-19> database using 'dbparser' package. It is a smaller version from 'dbdataset' package. It contains only information about COVID-19 possible treatment.
Maintained by Mohammed Ali. Last updated 11 months ago.
datasetdbparserdrugbankdrugbank-database
3.4 match 3 stars 4.48 score 6 scripts
rdinnager
phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs
The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.
Maintained by Russell Dinnage. Last updated 7 months ago.
3.6 match 1 stars 4.20 score 53 scripts 1 dependents
matthewabirk
respirometry:Tools for Conducting and Analyzing Respirometry Experiments
Provides tools to enable the researcher to more precisely conduct respirometry experiments. Strong emphasis is on aquatic respirometry. Tools focus on helping the researcher setup and conduct experiments. Functions for analysis of resulting respirometry data are also provided. This package provides tools for intermittent, flow-through, and closed respirometry techniques.
Maintained by Matthew A. Birk. Last updated 4 months ago.
5.7 match 2.61 score 68 scripts 1 dependents
remkoduursma
lgrdata:Example Datasets for a Learning Guide to R
A largish collection of example datasets, including several classics. Many of these datasets are well suited for regression, classification, and visualization.
Maintained by Remko Duursma. Last updated 6 years ago.
4.5 match 3.11 score 26 scripts
omarashkar
PKbioanalysis:Pharmacokinetic Bioanalysis Experiments Design and Exploration
Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations. The package impose regulatory constrains and sanity checking for common bioanalytical procedures. Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.
Maintained by Omar Elashkar. Last updated 5 months ago.
3.1 match 4.40 score 4 scripts
pdalgd
ISwR:Introductory Statistics with R
Data sets and scripts for text examples and exercises in P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Maintained by Peter Dalgaard. Last updated 5 months ago.
4.0 match 3.31 score 300 scriptsbioc
signifinder:Collection and implementation of public transcriptional cancer signatures
signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Maintained by Stefania Pirrotta. Last updated 2 months ago.
geneexpressiongenetargetimmunooncologybiomedicalinformaticsrnaseqmicroarrayreportwritingvisualizationsinglecellspatialgenesignaling
2.0 match 7 stars 6.28 score 15 scripts
cud2v
pccc:Pediatric Complex Chronic Conditions
An implementation of the pediatric complex chronic conditions (CCC) classification system using R and C++.
Maintained by Seth Russell. Last updated 5 months ago.
2.0 match 5 stars 5.93 score 38 scriptsbioc
famat:Functional analysis of metabolic and transcriptomic data
Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.
Maintained by Mathieu Charles. Last updated 5 months ago.
functionalpredictiongenesetenrichmentpathwaysgoreactomekeggcompoundgene-ontologygenesshiny
3.0 match 1 stars 3.78 score 2 scripts
huerqiang
prioGene:Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
In gene sequencing methods, the topological features of protein-protein interaction (PPI) networks are often used, such as ToppNet <https://toppgene.cchmc.org>. In this study, a candidate gene prioritization method was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease PPI networks with weights for nodes and edges based on functional information.
Maintained by Erqiang Hu. Last updated 5 years ago.
graphandnetworkfunctionalgenomicsgeneticsnetwork
3.8 match 3.00 score 10 scripts
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 11 days ago.
mass-spectrometrynon-targetcppopenjdk
1.8 match 65 stars 6.22 score 43 scripts
januarharianto
respR:Import, Process, Analyse, and Calculate Rates from Respirometry Data
Provides a structural, reproducible workflow for the processing and analysis of respirometry data. It contains analytical functions and utilities for working with oxygen time-series to determine respiration or oxygen production rates, and to make it easier to report and share analyses. See Harianto et al. 2019 <doi:10.1111/2041-210X.13162>.
Maintained by Nicholas Carey. Last updated 10 months ago.
1.7 match 12 stars 5.64 score 90 scriptsbioc
phantasus:Visual and interactive gene expression analysis
Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.
Maintained by Alexey Sergushichev. Last updated 5 months ago.
geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology
1.2 match 43 stars 7.68 score 15 scripts
mdbahadur
rhcoclust:Robust Hierarchical Co-Clustering to Identify Significant Co-Cluster
Here we performs robust hierarchical co-clustering between row and column entities of a data matrix in absence and presence of outlying observations. It can be used to explore important co-clusters consisting of important samples and their regulatory significant features. Please see Hasan, Badsha and Mollah (2020) <doi:10.1101/2020.05.13.094946>.
Maintained by Md. Bahadur Badsha. Last updated 2 years ago.
3.4 match 2.70 score 9 scriptsfmmattioni
whippr:Tools for Manipulating Gas Exchange Data
Set of tools for manipulating gas exchange data from cardiopulmonary exercise testing.
Maintained by Felipe Mattioni Maturana. Last updated 8 months ago.
1.9 match 12 stars 4.26 score 5 scripts
wleoncio
nutrition:Useful Functions for People on a Diet
Contains a collection of functions for performing different kinds of calculation that are of interest to someone following a diet plan. Calculators for the Basal Metabolic Rate are based on Mifflin et al. (1990) <doi:10.1093/ajcn/51.2.241> and McArdle, W. D., Katch, F. I., & Katch, V. L. (2010, ISBN:9780812109917).
Maintained by Waldir Leoncio. Last updated 1 years ago.
2.5 match 2.70 score
tkcaccia
MetChem:Chemical Structural Similarity Analysis
A new pipeline to explore chemical structural similarity across metabolite. It allows to classify metabolites in structurally-related modules and identify common shared functional groups. KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705>, Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>, and Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. (2023) Bioinformatics Advances <doi:10.1093/bioadv/vbad053>.
Maintained by Stefano Cacciatore. Last updated 2 years ago.
3.4 match 2.00 scorebioc
RITAN:Rapid Integration of Term Annotation and Network resources
Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.
Maintained by Michael Zimmermann. Last updated 5 months ago.
qualitycontrolnetworknetworkenrichmentnetworkinferencegenesetenrichmentfunctionalgenomicsgraphandnetwork
1.3 match 5.40 score 9 scripts
jorgedelro
MFO:Maximal Fat Oxidation and Kinetics Calculation
Calculate the maximal fat oxidation, the exercise intensity that elicits the maximal fat oxidation and the SIN model to represent the fat oxidation kinetics. Three variables can be obtained from the SIN model: dilatation, symmetry and translation. Examples of these methods can be found in Montes de Oca et al (2021) <doi:10.1080/17461391.2020.1788650> and Chenevière et al. (2009) <doi:10.1249/MSS.0b013e31819e2f91>.
Maintained by Jorge R Fernandez-Santos. Last updated 3 years ago.
2.0 match 2.70 score 2 scripts
jvanschalkwyk
corona:Coronavirus ('Rona') Data Exploration
Manipulate and view coronavirus data and other societally relevant data at a basic level.
Maintained by Jo van Schalkwyk. Last updated 4 years ago.
1.9 match 2.70 score 1 scripts
helenkettle
microPop:Process-Based Modelling of Microbial Populations
Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time. This version contains network visualisation functions.
Maintained by Helen Kettle. Last updated 3 years ago.
1.8 match 2.64 score 11 scripts
extremestats
DATAstudio:The Research Data Warehouse of Miguel de Carvalho
Pulls together a collection of datasets from Miguel de Carvalho research articles. Including, for example: - de Carvalho (2012) <doi:10.1016/j.jspi.2011.08.016>; - de Carvalho et al (2012) <doi:10.1080/03610926.2012.709905>; - de Carvalho et al (2012) <doi:10.1016/j.econlet.2011.09.007>); - de Carvalho and Davison (2014) <doi:10.1080/01621459.2013.872651>; - de Carvalho and Rua (2017) <doi:10.1016/j.ijforecast.2015.09.004>; - de Carvalho et al (2023) <doi:10.1002/sta4.560>; - de Carvalho et al (2022) <doi:10.1007/s13253-021-00469-9>; - Palacios et al (2024) <doi:10.1214/24-BA1420>.
Maintained by Miguel de Carvalho. Last updated 11 hours ago.
4.0 match 1.00 score 2 scriptsbioc
transcriptogramer:Transcriptional analysis based on transcriptograms
R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.
Maintained by Diego Morais. Last updated 5 months ago.
softwarenetworkvisualizationsystemsbiologygeneexpressiongenesetenrichmentgraphandnetworkclusteringdifferentialexpressionmicroarrayrnaseqtranscriptionimmunooncology
0.8 match 4 stars 4.81 score 9 scripts
jedick
canprot:Chemical Analysis of Proteins
Chemical analysis of proteins based on their amino acid compositions. Amino acid compositions can be read from FASTA files and used to calculate chemical metrics including carbon oxidation state and stoichiometric water content, as described in Dick et al. (2020) <doi:10.5194/bg-17-6145-2020>. Other properties that can be calculated include protein length, grand average of hydropathy (GRAVY), isoelectric point (pI), molecular weight (MW), standard molal volume (V0), and metabolic costs (Akashi and Gojobori, 2002 <doi:10.1073/pnas.062526999>; Wagner, 2005 <doi:10.1093/molbev/msi126>; Zhang et al., 2018 <doi:10.1038/s41467-018-06461-1>). A database of amino acid compositions of human proteins derived from UniProt is provided.
Maintained by Jeffrey Dick. Last updated 13 days ago.
amino-acid-compositionchemical-metricshydration-stateisoelectric-pointoxidation-stateproteins
0.5 match 3 stars 6.70 score 46 scripts 1 dependents
adwolfer
santaR:Short Asynchronous Time-Series Analysis
A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.
Maintained by Arnaud Wolfer. Last updated 1 years ago.
0.5 match 11 stars 6.44 score 63 scripts
danielebizzarri
MiMIR:Metabolomics-Based Models for Imputing Risk
Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Maintained by Daniele Bizzarri. Last updated 2 years ago.
binary-risk-factorsbiomarkerslinear-regressionmetabolitesmetabolomicsnightingale-metabolomicsrisk-factor-modelsrisk-factorssurrogate-models
0.8 match 8 stars 4.11 score 32 scripts
bioc
funOmics:Aggregating Omics Data into Higher-Level Functional Representations
The 'funOmics' package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!
Maintained by Elisa Gomez de Lope. Last updated 5 months ago.
softwaretranscriptomicsmetabolomicsproteomicspathwaysgokegg
0.5 match 5 stars 5.10 score 3 scripts
jamespeapen
ceas:Cellular Energetics Analysis Software
Measuring cellular energetics is essential to understanding a matrix’s (e.g. cell, tissue or biofluid) metabolic state. The Agilent Seahorse machine is a common method to measure real-time cellular energetics, but existing analysis tools are highly manual or lack functionality. The Cellular Energetics Analysis Software (ceas) R package fills this analytical gap by providing modular and automated Seahorse data analysis and visualization using the methods described by Mookerjee et al. (2017) <doi:10.1074/jbc.m116.774471>.
Maintained by Rachel House. Last updated 3 months ago.
0.5 match 1 stars 5.08 score 3 scripts
janlisec
CorMID:Correct Mass Isotopologue Distribution Vectors
In metabolic flux experiments tracer molecules (often glucose containing labelled carbon) are incorporated in compounds measured using mass spectrometry. The mass isotopologue distributions of these compounds needs to be corrected for natural abundance of labelled carbon and other effects, which are specific on the compound and ionization technique applied. This package provides functions to correct such effects in gas chromatography atmospheric pressure chemical ionization mass spectrometry analyses.
Maintained by Jan Lisec. Last updated 2 months ago.
0.5 match 4.88 score 3 scripts 1 dependents
zhao-jun-yong
aelab:Data Processing for Aquatic Ecology
Facilitate the analysis of data related to aquatic ecology, specifically the establishment of carbon budget. Currently, the package allows the below analysis. (i) the calculation of greenhouse gas flux based on data obtained from trace gas analyzer using the method described in Lin et al. (2024). (ii) the calculation of Dissolved Oxygen (DO) metabolism based on data obtained from dissolved oxygen data logger using the method described in Staehr et al. (2010). Yong et al. (2024) <doi:10.5194/bg-21-5247-2024>. Staehr et al. (2010) <doi:10.4319/lom.2010.8.0628>.
Maintained by Zhao-Jun Yong. Last updated 3 months ago.
0.5 match 4.54 score 2 scripts
bioc
qmtools:Quantitative Metabolomics Data Processing Tools
The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.
Maintained by Jaehyun Joo. Last updated 5 months ago.
metabolomicspreprocessingnormalizationdimensionreductionmassspectrometry
0.5 match 1 stars 4.30 score 5 scripts
sufyansuleman
InsuSensCalc:Insulin Sensitivity Indices Calculator
It facilitates the calculation of 40 different insulin sensitivity indices based on fasting, oral glucose tolerance test (OGTT), lipid (adipose), and tracer (palmitate and glycerol rate) and dxa (fat mass) measurement values. It enables easy and accurate assessment of insulin sensitivity, critical for understanding and managing metabolic disorders like diabetes and obesity. Indices calculated are described in Gastaldelli (2022). <doi:10.1002/oby.23503> and Lorenzo (2010). <doi:10.1210/jc.2010-1144>.
Maintained by Sufyan Suleman. Last updated 12 months ago.
0.5 match 1 stars 4.00 score 3 scripts
takouajendoubi
iCARH:Integrative Conditional Autoregressive Horseshoe Model
Implements the integrative conditional autoregressive horseshoe model discussed in Jendoubi, T., Ebbels, T.M. Integrative analysis of time course metabolic data and biomarker discovery. BMC Bioinformatics 21, 11 (2020) <doi:10.1186/s12859-019-3333-0>. The model consists in three levels: Metabolic pathways level modeling interdependencies between variables via a conditional auto-regressive (CAR) component, integrative analysis level to identify potential associations between heterogeneous omic variables via a Horseshoe prior and experimental design level to capture experimental design conditions through a mixed-effects model. The package also provides functions to simulate data from the model, construct pathway matrices, post process and plot model parameters.
Maintained by Takoua Jendoubi. Last updated 5 years ago.
0.8 match 2.00 score 6 scriptsjanlisec
MetabolomicsBasics:Basic Functions to Investigate Metabolomics Data Matrices
A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.
Maintained by Jan Lisec. Last updated 1 years ago.
0.5 match 3.00 score 3 scripts
samaneh-bioinformatics
BNrich:Pathway Enrichment Analysis Based on Bayesian Network
Maleknia et al. (2020) <doi:10.1101/2020.01.13.905448>. A novel pathway enrichment analysis package based on Bayesian network to investigate the topology features of the pathways. firstly, 187 kyoto encyclopedia of genes and genomes (KEGG) human non-metabolic pathways which their cycles were eliminated by biological approach, enter in analysis as Bayesian network structures. The constructed Bayesian network were optimized by the Least Absolute Shrinkage Selector Operator (lasso) and the parameters were learned based on gene expression data. Finally, the impacted pathways were enriched by Fisher’s Exact Test on significant parameters.
Maintained by Samaneh Maleknia. Last updated 5 years ago.
networkenrichmentgeneexpressionpathwaysbayesiankegg
0.5 match 3.00 score
cran
phoenics:Pathways Longitudinal and Differential Analysis in Metabolomics
Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.
Maintained by Camille Guilmineau. Last updated 2 months ago.
0.5 match 2.70 score
virgile-baudrot
rPBK:Inference and Prediction of Generic Physiologically-Based Kinetic Models
Fit and simulate any kind of physiologically-based kinetic ('PBK') models whatever the number of compartments. Moreover, it allows to account for any link between pairs of compartments, as well as any link of each of the compartments with the external medium. Such generic PBK models have today applications in pharmacology (PBPK models) to describe drug effects, in toxicology and ecotoxicology (PBTK models) to describe chemical substance effects. In case of exposure to a parent compound (drug or chemical) the 'rPBK' package allows to consider metabolites, whatever their number and their phase (I, II, ...). Last but not least, package 'rPBK' can also be used for dynamic flux balance analysis (dFBA) to deal with metabolic networks. See also Charles et al. (2022) <doi:10.1101/2022.04.29.490045>.
Maintained by Virgile Baudrot. Last updated 1 years ago.
0.5 match 2.70 score 3 scriptscran
HealthCal:Health Calculator
Health Calculator helps to find different parameters like basal metabolic rate, body mass index etc. related to fitness and health of a person.
Maintained by Pankaj Das. Last updated 2 years ago.
0.5 match 2.00 score
ruthckb
bubbleHeatmap:Produces 'bubbleHeatmap' Plots for Visualising Metabolomics Data
Plotting package based on the grid system, combining elements of a bubble plot and heatmap to conveniently display two numerical variables, (represented by color and size) grouped by categorical variables on the x and y axes. This is a useful alternative to a forest plot when the data can be grouped in two dimensions, such as predictors x outcomes. It has particular advantages for visualising the metabolic measures produced by the 'Nightingale Health' metabolomics platform, and templates are included for automatically generating figures from these datasets.
Maintained by Ruth Boxall. Last updated 2 years ago.
0.5 match 1 stars 2.00 score 3 scriptstkcaccia
musicNMR:Conversion of Nuclear Magnetic Resonance Spectra in Audio Files
A collection of functions for converting and visualization the free induction decay of mono dimensional nuclear magnetic resonance (NMR) spectra into an audio file. It facilitates the conversion of Bruker datasets in files WAV. The sound of NMR signals could provide an alternative to the current representation of the individual metabolic fingerprint and supply equally significant information. The package includes also NMR spectra of the urine samples provided by four healthy donors. Based on Cacciatore S, Saccenti E, Piccioli M. Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments. OMICS. 2015;19(3):147-56. <doi:10.1089/omi.2014.0131>.
Maintained by Stefano Cacciatore. Last updated 1 years ago.
0.8 match 1.00 score 4 scriptscran
wnl:Minimization Tool for Pharmacokinetic-Pharmacodynamic Data Analysis
This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Maintained by Kyun-Seop Bae. Last updated 25 days ago.
0.5 match 1 stars 1.48 score 6 scripts
syedhaider5
iDOS:Integrated Discovery of Oncogenic Signatures
A method to integrate molecular profiles of cancer patients (gene copy number and mRNA abundance) to identify candidate gain of function alterations. These candidate alterations can be subsequently further tested to discover cancer driver alterations. Briefly, this method tests of genomic correlates of mRNA dysregulation and prioritise those where DNA gains/amplifications are associated with elevated mRNA expression of the same gene. For details see, Haider S et al. (2016) "Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia", Genome Biology, <https://pubmed.ncbi.nlm.nih.gov/27358048/>.
Maintained by Syed Haider. Last updated 1 years ago.
0.5 match 1.00 score 10 scripts