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r-tfisher
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public |
We provide the cumulative distribution function (CDF), quantile, and statistical power calculator for a collection of thresholding Fisher's p-value combination methods, including Fisher's p-value combination method, truncated product method and, in particular, soft-thresholding Fisher's p-value combination method which is proven to be optimal in some context of signal detection. The p-value calculator for the omnibus version of these tests are also included. For reference, please see Hong Zhang and Zheyang Wu. "TFisher Tests: Optimal and Adaptive Thresholding for Combining p-Values", submitted.
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2025-09-24 |
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filepattern
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public |
Python library to store and filter files with systematic naming conventions using simplified regular expression-like patterns
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2025-09-24 |
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r-tarchetypes
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public |
Function-oriented Make-like declarative workflows for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible workflows concisely and compactly. The methods in this package were influenced by the 'drake' R package by Will Landau (2018) <doi:10.21105/joss.00550>.
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2025-09-24 |
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r-lsmeans
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Obtain least-squares means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays. Least-squares means were proposed in Harvey, W (1960) "Least-squares analysis of data with unequal subclass numbers", Tech Report ARS-20-8, USDA National Agricultural Library, and discussed further in Searle, Speed, and Milliken (1980) "Population marginal means in the linear model: An alternative to least squares means", The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>. NOTE: lsmeans now relies primarily on code in the 'emmeans' package. 'lsmeans' will be archived in the near future.
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2025-09-24 |
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r-networktoolbox
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Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
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2025-09-24 |
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r-diversity
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Allows the calculation of both genetic diversity partition statistics, genetic differentiation statistics, and locus informativeness for ancestry assignment. It also provides users with various option to calculate bootstrapped 95\% confidence intervals both across loci, for pairwise population comparisons, and to plot these results interactively. Parallel computing capabilities and pairwise results without bootstrapping are provided. Also calculates F-statistics from Weir and Cockerham (1984). Various plotting features are provided, as well as Chi-square tests of genetic heterogeneity. Functionality for the calculation of various diversity parameters is possible for RAD-seq derived SNP data sets containing thousands of marker loci. A shiny application for the development of microsatellite multiplexes is also available.
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2025-09-24 |
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stglib
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public |
Process data from a variety of oceanographic instrumentation
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2025-09-24 |
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vercel-cli
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public |
Vercel's frontend cloud gives developers frameworks, workflows, and infrastructure to build a faster, more personalized web.
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2025-09-24 |
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r-coxme
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public |
This package fits Cox proportional hazards models containing both fixed and random effects. The random effects can have a general form, of which familial interactions (a "kinship" matrix) is a particular special case. Note that the simplest case of a mixed effects Cox model, i.e. a single random per-group intercept, is also called a "frailty" model. The approach is based on Rippatti and Palgren, Biometrics 2002.
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2025-09-24 |
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sourmash-minimal
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public |
Compute and compare MinHash signatures for DNA data sets.
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2025-09-24 |
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r-policytree
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public |
Learn optimal policies via doubly robust empirical welfare maximization over trees. This package implements the multi-action doubly robust approach of Zhou, Athey and Wager (2018) <arXiv:1810.04778> in the case where we want to learn policies that belong to the class of depth k decision trees.
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2025-09-24 |
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r-dnapath
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Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.
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2025-09-24 |
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r-catnet
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public |
Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
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2025-09-24 |
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taxcalc
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public |
open-source microsimulation model for static analysis of USA federal income and payroll taxes.
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2025-09-24 |
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r-bibliometrix
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public |
Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
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2025-09-24 |
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r-scrime
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public |
Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.
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2025-09-24 |
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r-netrankr
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Implements methods for centrality related analyses of networks. While the package includes the possibility to build more than 20 indices, its main focus lies on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. These partial rankings can be analyzed with different methods, including probabilistic methods like computing expected node ranks and relative rank probabilities (how likely is it that a node is more central than another?). The methodology is described in depth in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
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2025-09-24 |
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r-bnstruct
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Bayesian Network Structure Learning from Data with Missing Values. The package implements the Silander-Myllymaki complete search, the Max-Min Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic searches, and the Structural Expectation-Maximization algorithm. Available scoring functions are BDeu, AIC, BIC. The package also implements methods for generating and using bootstrap samples, imputed data, inference.
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2025-09-24 |
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r-cvxbiclustr
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An iterative algorithm for solving a convex formulation of the biclustering problem.
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2025-09-24 |
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r-repmis
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Tools to load 'R' packages and automatically generate BibTeX files citing them as well as load and cache plain-text and 'Excel' formatted data stored on 'GitHub', and from other sources.
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2025-09-24 |
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r-integr
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Generates a 'Graphviz' graph of the most significant 3-way interaction gains (i.e. conditional information gains) based on a provided discrete data frame. Various output formats are supported ('Graphviz', SVG, PNG, PDF, PS). For references, see the webpage of Aleks Jakulin <http://stat.columbia.edu/~jakulin/Int/>.
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2025-09-24 |
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r-freqprof
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Tools for generating an informative type of line graph, the frequency profile, which allows single behaviors, multiple behaviors, or the specific behavioral patterns of individual subjects to be graphed from occurrence/nonoccurrence behavioral data.
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2025-09-24 |
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r-slim
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Fits singular linear models to longitudinal data. Singular linear models are useful when the number, or timing, of longitudinal observations may be informative about the observations themselves. They are described in Farewell (2010) <doi:10.1093/biomet/asp068>, and are extensions of the linear increments model <doi:10.1111/j.1467-9876.2007.00590.x> to general longitudinal data.
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2025-09-24 |
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r-redshifttools
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Efficiently upload data into an Amazon Redshift database using the approach recommended by Amazon <https://aws.amazon.com/es/redshift/>.
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2025-09-24 |
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r-htm2txt
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Convert a html document to simple plain texts by removing all html tags. This package utilizes regular expressions to strip off html tags. It also offers gettxt() and browse() function, which enables you to get or browse texts at a certain web page.
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2025-09-24 |
