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bioc

ISLET:Individual-Specific ceLl typE referencing Tool

ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.

Maintained by Hao Feng. Last updated 5 months ago.

softwarernaseqtranscriptomicstranscriptionsequencinggeneexpressiondifferentialexpressiondifferentialmethylation

4.00 score 9 scripts

ebmtnprof

rties:Modeling Interpersonal Dynamics

The name of this package grew out of our research on temporal interpersonal emotion systems (TIES), hence 'rties'. It provides tools for using a set of models to investigate temporal processes in bivariate (e.g., dyadic) systems. The general approach is to model, one dyad at a time, the dynamics of a variable that is assessed repeatedly from both partners, extract the parameter estimates for each dyad, and then use those parameter estimates as input to a latent profile analysis to extract groups of dyads with qualitatively distinct dynamics. Finally, the profile memberships can be used to either predict, or be predicted by, another variable of interest. Currently, 2 models are supported: 1) inertia-coordination, and 2) a coupled-oscillator. Extended documentation is provided in vignettes. Theoretical background can be found in Butler (2011) <doi:10.1177/1088868311411164> and Butler & Barnard (2019) <doi:10.1097/PSY.0000000000000703>.

Maintained by Emily Butler. Last updated 3 years ago.

11 stars 3.94 score 16 scripts

vonnwalter23

DiNAMIC.Duo:Finding Recurrent DNA Copy Number Alterations and Differences

In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022) can be found at <doi: 10.1093/bioinformatics/btac542>.

Maintained by Vonn Walter. Last updated 2 years ago.

biomart

2.70 score

cran

spc4sts:Statistical Process Control for Stochastic Textured Surfaces

Provides statistical process control tools for stochastic textured surfaces. The current version supports the following tools: (1) generic modeling of stochastic textured surfaces. (2) local defect monitoring and diagnostics in stochastic textured surfaces, which was proposed by Bui and Apley (2018a) <doi:10.1080/00401706.2017.1302362>. (3) global change monitoring in the nature of stochastic textured surfaces, which was proposed by Bui and Apley (2018b) <doi:10.1080/00224065.2018.1507559>. (4) computation of dissimilarity matrix of stochastic textured surface images, which was proposed by Bui and Apley (2019b) <doi:10.1016/j.csda.2019.01.019>.

Maintained by Anh Tuan Bui. Last updated 3 years ago.

1.00 score

cran

vitality:Fitting Routines for the Vitality Family of Mortality Models

Provides fitting routines for four versions of the Vitality family of mortality models.

Maintained by David J. Sharrow. Last updated 7 years ago.

1.00 score

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