R-universe search: exports:zscore

Showing 14 of total 14 results (show query)

bioc

limma:Linear Models for Microarray and Omics Data

Data analysis, linear models and differential expression for omics data.

Maintained by Gordon Smyth. Last updated 11 days ago.

exonarray geneexpression transcription alternativesplicing differentialexpression differentialsplicing genesetenrichment dataimport bayesian clustering regression timecourse microarray micrornaarray mrnamicroarray onechannel proprietaryplatforms twochannel sequencing rnaseq batcheffect multiplecomparison normalization preprocessing qualitycontrol biomedicalinformatics cellbiology cheminformatics epigenetics functionalgenomics genetics immunooncology metabolomics proteomics systemsbiology transcriptomics

13.81 score 16k scripts 586 dependents

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

93 stars 13.32 score 7.2k scripts 7 dependents

asardaes

dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

262 stars 12.35 score 406 scripts 14 dependents

atsa-es

MARSS:Multivariate Autoregressive State-Space Modeling

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models, including partially deterministic models. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Fitting available via Expectation-Maximization (EM), BFGS (using optim), and 'TMB' (using the 'marssTMB' companion package). Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, model selection criteria including bootstrap AICb, confidences intervals via the Hessian approximation or bootstrapping, and all conditional residual types. See the user guide for examples of dynamic factor analysis, dynamic linear models, outlier and shock detection, and multivariate AR-p models. Online workshops (lectures, eBook, and computer labs) at <https://atsa-es.github.io/>.

Maintained by Elizabeth Eli Holmes. Last updated 1 years ago.

multivariate-timeseries state-space-models statistics time-series

52 stars 10.34 score 596 scripts 3 dependents

poissonconsulting

extras:Helper Functions for Bayesian Analyses

Functions to 'numericise' 'R' objects (coerce to numeric objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and calculate deviance residuals as well as 'R' translations of some 'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.

Maintained by Nicole Hill. Last updated 2 months ago.

9 stars 8.49 score 15 scripts 16 dependents

oobianom

quickcode:Quick and Essential 'R' Tricks for Better Scripts

The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.

Maintained by Obinna Obianom. Last updated 27 days ago.

colors data distributions images

5 stars 7.76 score 7 scripts 6 dependents

poissonconsulting

mcmcr:Manipulate MCMC Samples

Functions and classes to store, manipulate and summarise Monte Carlo Markov Chain (MCMC) samples. For more information see Brooks et al. (2011) <isbn:978-1-4200-7941-8>.

Maintained by Joe Thorley. Last updated 2 months ago.

coda mcmc

17 stars 7.66 score 111 scripts 10 dependents

poissonconsulting

nlist:Lists of Numeric Atomic Objects

Create and manipulate numeric list ('nlist') objects. An 'nlist' is an S3 list of uniquely named numeric objects. An numeric object is an integer or double vector, matrix or array. An 'nlists' object is a S3 class list of 'nlist' objects with the same names, dimensionalities and typeofs. Numeric list objects are of interest because they are the raw data inputs for analytic engines such as 'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are useful for storing multiple realizations of of simulated data sets, can be converted to coda::mcmc and coda::mcmc.list objects.

Maintained by Joe Thorley. Last updated 2 months ago.

data-frame natomic nlist nlists

6 stars 7.23 score 13 scripts 12 dependents

cefet-rj-dal

daltoolbox:Leveraging Experiment Lines to Data Analytics

The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_20>.

Maintained by Eduardo Ogasawara. Last updated 2 months ago.

1 stars 6.65 score 536 scripts 4 dependents

stamats

MKdescr:Descriptive Statistics

Computation of standardized interquartile range (IQR), Huber-type skipped mean (Hampel (1985), <doi:10.2307/1268758>), robust coefficient of variation (CV) (Arachchige et al. (2019), <arXiv:1907.01110>), robust signal to noise ratio (SNR), z-score, standardized mean difference (SMD), as well as functions that support graphical visualization such as boxplots based on quartiles (not hinges), negative logarithms and generalized logarithms for 'ggplot2' (Wickham (2016), ISBN:978-3-319-24277-4).

Maintained by Matthias Kohl. Last updated 1 years ago.

3 stars 6.02 score 47 scripts 5 dependents

bioc

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.

software dataimport preprocessing dimensionreduction principalcomponent regression differentialexpression genesetenrichment transcriptomics transcription geneexpression rnaseq microarray proteomics metabolomics massspectrometry

5.89 score 5 scripts

rezamoammadi

liver:"Eating the Liver of Data Science"

Provides a suite of helper functions and a collection of datasets used in the book <https://uncovering-data-science.netlify.app>. It is designed to make data science techniques accessible to individuals with minimal coding experience. Inspired by an ancient Persian idiom, the package likens this learning process to "eating the liver of data science," symbolizing deep and immersive engagement with the field.

Maintained by Reza Mohammadi. Last updated 12 days ago.

4.13 score 67 scripts

amlinz

OTUtable:North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Analyses of OTU tables produced by 16S rRNA gene amplicon sequencing, as well as example data. It contains the data and scripts used in the paper Linz, et al. (2017) "Bacterial community composition and dynamics spanning five years in freshwater bog lakes," <doi: 10.1128/mSphere.00169-17>.

Maintained by Alexandra Linz. Last updated 7 years ago.

2.20 score 53 scripts

arissyntakas

GeneScoreR:Gene Scoring from Count Tables

Provides two methods for automatic calculation of gene scores from gene count tables: the z-score method, which requires a table of samples being scored and a count table with control samples, and the geometric mean method, which does not rely on control samples. The mathematical methods implemented are described by Kim et al. (2018) <doi:10.1089/jir.2017.0127>.

Maintained by Aris Syntakas. Last updated 5 months ago.

1.00 score