isglobal-exposomehub.r-universe.dev

[isglobal-exposomehub] BigDataStatMeth 2.0.2

dolors.pelegri@isglobal.org (Dolors Pelegri-Siso) — Mon, 08 Jun 2026 16:31:51 GMT

A framework for 'scalable' statistical computing on large on-disk matrices stored in 'HDF5' files. It provides efficient block-wise implementations of core linear-algebra operations (matrix multiplication, SVD, PCA, QR decomposition, and canonical correlation analysis) written in C++ and R. These building blocks are designed not only for direct use, but also as foundational components for developing new statistical methods that must operate on datasets too large to fit in memory. The package supports data provided either as 'HDF5' files or standard R objects, and is intended for high-dimensional applications such as 'omics' and precision-medicine research.

[bioc] epimutacions 1.17.0

dolors.pelegri@isglobal.org (Dolors Pelegri-Siso) — Tue, 28 Apr 2026 12:58:12 GMT

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

[bioc] methylclock 1.19.0

dolors.pelegri@isglobal.org (Dolors Pelegri-Siso) — Tue, 28 Apr 2026 12:56:26 GMT

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

[bioc] scoreInvHap 1.35.0

dolors.pelegri@isglobal.org (Dolors Pelegri-Siso) — Tue, 28 Apr 2026 12:45:54 GMT

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.

[bioc] tweeDEseq 1.59.0

dolors.pelegri@isglobal.org (Dolors Pelegri-Siso) — Tue, 28 Apr 2026 12:36:03 GMT

Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.

[isglobal-brge] SNPassoc 2.3.1

dolors.pelegri@isglobal.org (Dolors Pelegri) — Mon, 13 Apr 2026 08:38:45 GMT

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 . This version includes internal copies of functions from the archived 'haplo.stats' package to maintain functionality.