Showing 13 of total 13 results (show query)
r-forge
copula:Multivariate Dependence with Copulas
Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Maintained by Martin Maechler. Last updated 25 days ago.
11.83 score 1.2k scripts 86 dependents
bioc
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
41 stars 8.50 score 155 scripts
antoinelucas64
amap:Another Multidimensional Analysis Package
Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).
Maintained by Antoine Lucas. Last updated 5 months ago.
7.73 score 460 scripts 26 dependentsbioc
PICS:Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
Maintained by Renan Sauteraud. Last updated 4 days ago.
clusteringvisualizationsequencingchipseqgsl
6.43 score 7 scripts 1 dependents
comeetie
greed:Clustering and Model Selection with the Integrated Classification Likelihood
An ensemble of algorithms that enable the clustering of networks and data matrices (such as counts, categorical or continuous) with different type of generative models. Model selection and clustering is performed in combination by optimizing the Integrated Classification Likelihood (which is equivalent to minimizing the description length). Several models are available such as: Stochastic Block Model, degree corrected Stochastic Block Model, Mixtures of Multinomial, Latent Block Model. The optimization is performed thanks to a combination of greedy local search and a genetic algorithm (see <arXiv:2002:11577> for more details).
Maintained by Etienne Côme. Last updated 2 years ago.
14 stars 5.94 score 41 scriptsbioc
betaHMM:A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data
A novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites.
Maintained by Koyel Majumdar. Last updated 3 months ago.
dnamethylationdifferentialmethylationimmunooncologybiomedicalinformaticsmethylationarraysoftwaremultiplecomparisonsequencingspatialcoveragegenetargethiddenmarkovmodelmicroarray
4.18 score
cran
randomizeR:Randomization for Clinical Trials
This tool enables the user to choose a randomization procedure based on sound scientific criteria. It comprises the generation of randomization sequences as well the assessment of randomization procedures based on carefully selected criteria. Furthermore, 'randomizeR' provides a function for the comparison of randomization procedures.
Maintained by Ralf-Dieter Hilgers. Last updated 2 years ago.
2 stars 3.38 score 1 dependents
kcha193
infoDecompuTE:Information Decomposition of Two-Phase Experiments
The main purpose of this package is to generate the structure of the analysis of variance (ANOVA) table of the two-phase experiments. The user only need to input the design and the relationships of the random and fixed factors using the Wilkinson-Rogers' syntax, this package can then quickly generate the structure of the ANOVA table with the coefficients of the variance components for the expected mean squares. Thus, the balanced incomplete block design and provides the efficiency factors of the fixed effects can also be studied and compared much easily.
Maintained by Kevin Chang. Last updated 5 years ago.
3.15 score 28 scripts
sandrinepavoine
adiv:Analysis of Diversity
Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Maintained by Sandrine Pavoine. Last updated 1 years ago.
1 stars 2.28 score 63 scripts
cran
hdthreshold:Inference on Many Jumps in Nonparametric Panel Regression Models
Provides uniform testing procedures for existence and heterogeneity of threshold effects in high-dimensional nonparametric panel regression models. The package accompanies the paper Chen, Keilbar, Su and Wang (2023) "Inference on many jumps in nonparametric panel regression models". arXiv preprint <doi:10.48550/arXiv.2312.01162>.
Maintained by Georg Keilbar. Last updated 3 months ago.
1.00 score