methylclock - Chronological, Gestational and Biological DNAm Age Estimation with Methylation-Based Clocks
Estimates chronological, gestational and biological DNA methylation (DNAm) age, trait scores and epigenetic age acceleration from methylation beta values. Implements 44 published clocks, selectable by name, family or array platform: chronological (Horvath, Hannum, BNN, skin+blood, PedBE, Wu, AltumAge and others, including the cross-platform Garma clock native to EPICv2), gestational (Knight, Bohlin, Mayne, Lee, NEOage), phenotypic and pace-of-aging (Levine, DunedinPACE), telomere length, mitotic counters (epiTOC1/epiTOC2, HypoClock, stemTOC, RepliTali), causal (CausAge, DamAge, AdaptAge) and trait EpiScores. Accepts matrices, data frames, Bioconductor containers or HDF5 files, computing block-wise out-of-core through BigDataStatMeth when the data exceed memory. Provides configurable missing-value imputation (mean, reference or KNN), cell-type deconvolution, intrinsic and extrinsic epigenetic age acceleration (IEAA, EEAA), quality-control reports and plotting functions.
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dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationopenblascurlopensslcppopenmp
7.56 score 55 stars 83 scripts 786 downloads
epimutacions - Robust outlier identification for DNA methylation data
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.
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dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
5.53 score 38 scripts 456 downloadsmethylclockData - Data for methylclock package
Data resources used by the methylclock package to estimate chronological, gestational and biological age from DNA methylation, and to adjust those estimates for blood cell composition. It provides the coefficient tables of the individual clocks, the CpG sets of the mitotic counters, the weights of the neural network clock, and example methylation datasets. It also provides nine cell type reference datasets (andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord blood gse68456, gervin and lyle cord blood, guintivano dlpfc, saliva gse48472), downloaded from meffil (https://github.com/perishky/meffil/), which are used to estimate cell counts for the extrinsic epigenetic age acceleration (EEAA) method. All resources are served through ExperimentHub.
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specimensourceexperimenthubtissueorganismdatahomo_sapiens_datadatapkg
5.36 score 19 scriptstweeDEseq - RNA-seq data analysis using the Poisson-Tweedie family of distributions
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.
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immunooncologystatisticalmethoddifferentialexpressionsequencingrnaseqdnaseq
4.97 score 1 stars 1 dependents 52 scripts 574 downloadsmgcca - Generalized Canonical Correlation Analysis with Missing Individuals
Implements Generalized Canonical Correlation Analysis (GCCA) with missing individuals (whole missing rows; van de Velden and Bijmolt, 2006) for multi-block omics integration. The package operates directly on HDF5 matrices via the BigDataStatMeth C++ API to scale computations; R functions are thin wrappers around the C++ core.
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statisticalmethoddimensionreductionprincipalcomponentgeneexpressiontranscriptomicsepigeneticsmetabolomicsopenblascurlopensslcppopenmp
4.20 score 6 scriptssurvrec - Survival Analysis for Recurrent Event Data
Estimation of the survival function of inter-occurrence times for recurrent event data, using the estimators of Peña, Strawderman and Hollander (2001) <doi:10.1198/016214501753381922> and Wang and Chang (1999) <doi:10.1080/01621459.1999.10473831>, and maximum likelihood estimation under a gamma frailty model. Includes bootstrap comparison of survival quantiles between groups.
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cppopenmp
4.18 score 1 stars 48 downloadstweeDEseqCountData - RNA-seq count data employed in the vignette of the tweeDEseq package
RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package.
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genomehomo_sapiens_datarnaseqdatadatapkg
3.95 score 45 scripts