Showing 21 of total 21 results (show query)
lrberge
fixest:Fast Fixed-Effects Estimations
Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Maintained by Laurent Berge. Last updated 7 months ago.
394 stars 14.69 score 3.8k scripts 26 dependents
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 15 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
196 stars 14.31 score 984 scripts 11 dependentsbioc
Spectra:Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 22 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry
41 stars 13.01 score 254 scripts 35 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 15 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
131 stars 12.76 score 772 scripts 36 dependents
r-lum
Luminescence:Comprehensive Luminescence Dating Data Analysis
A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Maintained by Sebastian Kreutzer. Last updated 1 days ago.
bayesian-statisticsdata-sciencegeochronologyluminescenceluminescence-datingopen-scienceoslplottingradiofluorescencetlxsygcpp
15 stars 10.66 score 178 scripts 8 dependentsbioc
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 8 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils
16 stars 10.57 score 41 scripts 71 dependents
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 8 days ago.
9 stars 10.47 score 200 scripts 2 dependentsbioc
Cardinal:A mass spectrometry imaging toolbox for statistical analysis
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Maintained by Kylie Ariel Bemis. Last updated 3 months ago.
softwareinfrastructureproteomicslipidomicsmassspectrometryimagingmassspectrometryimmunooncologynormalizationclusteringclassificationregression
48 stars 10.32 score 200 scriptsbioc
ProtGenerics:Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
Maintained by Laurent Gatto. Last updated 2 months ago.
infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics
8 stars 9.36 score 4 scripts 188 dependents
vonjd
OneR:One Rule Machine Learning Classification Algorithm with Enhancements
Implements the One Rule (OneR) Machine Learning classification algorithm (Holte, R.C. (1993) <doi:10.1023/A:1022631118932>) with enhancements for sophisticated handling of numeric data and missing values together with extensive diagnostic functions. It is useful as a baseline for machine learning models and the rules are often helpful heuristics.
Maintained by Holger von Jouanne-Diedrich. Last updated 7 years ago.
40 stars 8.61 score 296 scripts 2 dependentsbioc
monaLisa:Binned Motif Enrichment Analysis and Visualization
Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.
Maintained by Michael Stadler. Last updated 5 days ago.
motifannotationvisualizationfeatureextractionepigenetics
40 stars 8.10 score 53 scripts
ekstroem
MESS:Miscellaneous Esoteric Statistical Scripts
A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book. See Ekstrøm, C. T. (2016). The R Primer. 2nd edition. Chapman & Hall.
Maintained by Claus Thorn Ekstrøm. Last updated 1 months ago.
biostatisticspower-analysisstatistical-analysisstatistical-methodsstatistical-modelsopenblascpp
4 stars 7.69 score 328 scripts 13 dependents
nicchr
cheapr:Simple Functions to Save Time and Memory
Fast and memory-efficient (or 'cheap') tools to facilitate efficient programming, saving time and memory. It aims to provide 'cheaper' alternatives to common base R functions, as well as some additional functions.
Maintained by Nick Christofides. Last updated 2 days ago.
19 stars 7.21 score 73 scripts 2 dependentsbioc
autonomics:Unified Statistical Modeling of Omics Data
This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs.
Maintained by Aditya Bhagwat. Last updated 2 months ago.
softwaredataimportpreprocessingdimensionreductionprincipalcomponentregressiondifferentialexpressiongenesetenrichmenttranscriptomicstranscriptiongeneexpressionrnaseqmicroarrayproteomicsmetabolomicsmassspectrometry
5.95 score 5 scripts
garybaylor
mixR:Finite Mixture Modeling for Raw and Binned Data
Performs maximum likelihood estimation for finite mixture models for families including Normal, Weibull, Gamma and Lognormal by using EM algorithm, together with Newton-Raphson algorithm or bisection method when necessary. It also conducts mixture model selection by using information criteria or bootstrap likelihood ratio test. The data used for mixture model fitting can be raw data or binned data. The model fitting process is accelerated by using R package 'Rcpp'.
Maintained by Youjiao Yu. Last updated 6 months ago.
8 stars 5.66 score 95 scripts 1 dependents
tweedell
motoRneuron:Analyzing Paired Neuron Discharge Times for Time-Domain Synchronization
The temporal relationship between motor neurons can offer explanations for neural strategies. We combined functions to reduce neuron action potential discharge data and analyze it for short-term, time-domain synchronization. Even more so, motoRneuron combines most available methods for the determining cross correlation histogram peaks and most available indices for calculating synchronization into simple functions. See Nordstrom, Fuglevand, and Enoka (1992) <doi:10.1113/jphysiol.1992.sp019244> for a more thorough introduction.
Maintained by Andrew Tweedell. Last updated 6 years ago.
1 stars 3.74 score 11 scripts
bentaylor1
miscFuncs:Miscellaneous Useful Functions Including LaTeX Tables, Kalman Filtering, QQplots with Simulation-Based Confidence Intervals, Linear Regression Diagnostics and Development Tools
Implementing various things including functions for LaTeX tables, the Kalman filter, QQ-plots with simulation-based confidence intervals, linear regression diagnostics, web scraping, development tools, relative risk and odds rati, GARCH(1,1) Forecasting.
Maintained by Benjamin M. Taylor. Last updated 5 months ago.
2.48 score 8 scripts
dzhang777
SlideCNA:Calls Copy Number Alterations from Slide-Seq Data
This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").
Maintained by Diane Zhang. Last updated 2 months ago.
1.70 score 3 scripts
doer0
doofa:Designs for Order-of-Addition Experiments
A facility to generate efficient designs for order-of-additions experiments under pair-wise-order model, see Dennis K. J. Lin and Jiayu Peng (2019)."Order-of-addition experiments: A review and some new thoughts". Quality Engineering, 31:1, 49-59, <doi:10.1080/08982112.2018.1548021>. It also provides a facility to generate component orthogonal arrays under component position model, see Jian-Feng Yang, Fasheng Sun & Hongquan Xu (2020): "A Component Position Model, Analysis and Design for Order-of-Addition Experiments". Technometrics, <doi:10.1080/00401706.2020.1764394>.
Maintained by Baidya Nath Mandal. Last updated 11 months ago.
1.48 score 1 dependents
cran
GAGBLUP:Genetic Algorithm Assisted Genomic Best Liner Unbiased Prediction
Performs genetic algorithm (Scrucca, L (2013) <doi:10.18637/jss.v053.i04>) assisted genomic best liner unbiased prediction for genomic selection. It also provides a binning method in natural population for genomic selection under the principle of linkage disequilibrium for dimensional reduction.
Maintained by Yuxiang Zhang. Last updated 2 years ago.
1.00 scorecran
BayesBP:Bayesian Estimation using Bernstein Polynomial Fits Rate Matrix
Smoothed lexis diagrams with Bayesian method specifically tailored to cancer incidence data. Providing to calculating slope and constructing credible interval. LC Chien et al. (2015) <doi:10.1080/01621459.2015.1042106>. LH Chien et al. (2017) <doi:10.1002/cam4.1102>.
Maintained by Li-Syuan Hong. Last updated 5 years ago.
1.00 score