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bioc

scRepertoire:A toolkit for single-cell immune receptor profiling

scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.

Maintained by Nick Borcherding. Last updated 10 days ago.

softwareimmunooncologysinglecellclassificationannotationsequencingcpp

327 stars 10.42 score 240 scripts

fbartos

zcurve:An Implementation of Z-Curves

An implementation of z-curves - a method for estimating expected discovery and replicability rates on the bases of test-statistics of published studies. The package provides functions for fitting the new density and EM version (Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>), censored observations, as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>). Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects. See the aforementioned articles for more information about the z-curves, expected discovery and replicability rates, validation studies, and limitations.

Maintained by František Bartoš. Last updated 10 months ago.

edrerrreplicabilityz-cruvecpp

12 stars 5.48 score 21 scripts 1 dependents

cotima

CoTiMA:Continuous Time Meta-Analysis ('CoTiMA')

The 'CoTiMA' package performs meta-analyses of correlation matrices of repeatedly measured variables taken from studies that used different time intervals. Different time intervals between measurement occasions impose problems for meta-analyses because the effects (e.g. cross-lagged effects) cannot be simply aggregated, for example, by means of common fixed or random effects analysis. However, continuous time math, which is applied in 'CoTiMA', can be used to extrapolate or intrapolate the results from all studies to any desired time lag. By this, effects obtained in studies that used different time intervals can be meta-analyzed. 'CoTiMA' fits models to empirical data using the structural equation model (SEM) package 'ctsem', the effects specified in a SEM are related to parameters that are not directly included in the model (i.e., continuous time parameters; together, they represent the continuous time structural equation model, CTSEM). Statistical model comparisons and significance tests are then performed on the continuous time parameter estimates. 'CoTiMA' also allows analysis of publication bias (Egger's test, PET-PEESE estimates, zcurve analysis etc.) and analysis of statistical power (post hoc power, required sample sizes). See Dormann, C., Guthier, C., & Cortina, J. M. (2019) <doi:10.1177/1094428119847277>. and Guthier, C., Dormann, C., & Voelkle, M. C. (2020) <doi:10.1037/bul0000304>.

Maintained by Markus Homberg. Last updated 6 days ago.

4 stars 5.26 score

davidvandijcke

DiSCos:Distributional Synthetic Controls Estimation

The method of synthetic controls is a widely-adopted tool for evaluating causal effects of policy changes in settings with observational data. In many settings where it is applicable, researchers want to identify causal effects of policy changes on a treated unit at an aggregate level while having access to data at a finer granularity. This package implements a simple extension of the synthetic controls estimator, developed in Gunsilius (2023) <doi:10.3982/ECTA18260>, that takes advantage of this additional structure and provides nonparametric estimates of the heterogeneity within the aggregate unit. The idea is to replicate the quantile function associated with the treated unit by a weighted average of quantile functions of the control units. The package contains tools for aggregating and plotting the resulting distributional estimates, as well as for carrying out inference on them.

Maintained by David Van Dijcke. Last updated 17 days ago.

1 stars 4.81 score 8 scripts

bioc

powerTCR:Model-Based Comparative Analysis of the TCR Repertoire

This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.

Maintained by Hillary Koch. Last updated 5 months ago.

softwareclusteringbiomedicalinformatics

4.00 score 4 scripts

cran

GRIDCOPULA:Bivariate Copula Functions Based on Regular Grid

Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.

Maintained by Rogelio Salinas Gutiérrez. Last updated 12 months ago.

2.18 score 1 dependents

cran

MLCOPULA:Classification Models with Copula Functions

Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.

Maintained by Rogelio Salinas Gutiérrez. Last updated 5 months ago.

2.00 score

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