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r-widyr
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Encapsulates the pattern of untidying data into a wide matrix, performing some processing, then turning it back into a tidy form. This is useful for several operations such as co-occurrence counts, correlations, or clustering that are mathematically convenient on wide matrices.
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2025-09-23 |
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r-geniebpc
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public |
The American Association Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) BioPharma Collaborative represents a multi-year, multi-institution effort to build a pan-cancer repository of linked clinico-genomic data. The genomic and clinical data are provided in multiple releases (separate releases for each cancer cohort with updates following data corrections), which are stored on the data sharing platform 'Synapse' <https://www.synapse.org/>. The 'genieBPC' package provides a seamless way to obtain the data corresponding to each release from 'Synapse' and to prepare datasets for analysis.
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2025-09-23 |
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python-docs-theme
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The Sphinx theme for the CPython docs and related projects
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2025-09-23 |
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r-phylotools
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A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.
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2025-09-23 |
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r-rpivottable
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public |
Build powerful pivot tables (aka Pivot Grid, Pivot Chart, Cross-Tab) and dynamically slice & dice / drag 'n' drop your data. 'rpivotTable' is a wrapper of 'pivottable', a powerful open-source Pivot Table library implemented in 'JavaScript' by Nicolas Kruchten. Aligned to 'pivottable' v2.19.0.
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2025-09-23 |
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pyrefly
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A fast type checker and IDE for Python
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2025-09-23 |
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r-texreg
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Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. (If the Zelig package, which this package enhances, cannot be found on CRAN, you can find it at <https://github.com/IQSS/Zelig>.)
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2025-09-23 |
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r-details
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Create a details HTML tag around R objects to place in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
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2025-09-23 |
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r-adabag
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It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done. Since version 2.0 the function margins() is available to calculate the margins for these classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as a function of the number of iterations. In addition, the ensembles can be pruned using the option 'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probability of each class for observations can be obtained. Version 3.1 modifies the relative importance measure to take into account the gain of the Gini index given by a variable in each tree and the weights of these trees. Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo and Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover, three new plots are also available importanceplot(), plot.errorevol() and plot.margins(). Version 4.1 allows to predict on unlabeled data. Version 4.2 includes the parallel computation option for some of the functions.
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2025-09-23 |
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r-rhub
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R-hub v2 uses GitHub Actions to run 'R CMD check' and similar package checks. The 'rhub' package helps you set up R-hub v2 for your R package, and start running checks.
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2025-09-23 |
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r-tidytree
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Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
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2025-09-23 |
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r-listarrays
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A toolbox for R arrays. Flexibly split, bind, reshape, modify, subset and name arrays.
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2025-09-23 |
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r-iheatmapr
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public |
Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.
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2025-09-23 |
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r-robustrankaggreg
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Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation (Kolde et. al in preparation) and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
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2025-09-23 |
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fedfred
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A feature-rich python package for interacting with the Federal Reserve Bank of St. Louis Economic Database (FRED)
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2025-09-23 |
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cherry-picker
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public |
Backport CPython changes from main to maintenance branches
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2025-09-23 |
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r-purrrlyr
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Some functions at the intersection of 'dplyr' and 'purrr' that formerly lived in 'purrr'.
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2025-09-23 |
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r-primme
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public |
R interface to PRIMME, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix. It can also compute singular values and vectors of a square or rectangular matrix. It can find largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence.
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2025-09-23 |
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r-rocit
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Sensitivity (or recall or true positive rate), false positive rate, specificity, precision (or positive predictive value), negative predictive value, misclassification rate, accuracy, F-score- these are popular metrics for assessing performance of binary classifier for certain threshold. These metrics are calculated at certain threshold values. Receiver operating characteristic (ROC) curve is a common tool for assessing overall diagnostic ability of the binary classifier. Unlike depending on a certain threshold, area under ROC curve (also known as AUC), is a summary statistic about how well a binary classifier performs overall for the classification task. ROCit package provides flexibility to easily evaluate threshold-bound metrics. Also, ROC curve, along with AUC, can be obtained using different methods, such as empirical, binormal and non-parametric. ROCit encompasses a wide variety of methods for constructing confidence interval of ROC curve and AUC. ROCit also features the option of constructing empirical gains table, which is a handy tool for direct marketing. The package offers options for commonly used visualization, such as, ROC curve, KS plot, lift plot. Along with in-built default graphics setting, there are rooms for manual tweak by providing the necessary values as function arguments. ROCit is a powerful tool offering a range of things, yet it is very easy to use.
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2025-09-22 |
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r-naniar
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public |
Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. 'naniar' provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of 'ggplot2' and tidy data.
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2025-09-22 |
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r-mcl
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Contains the Markov cluster algorithm (MCL) for identifying clusters in networks and graphs. The algorithm simulates random walks on a (n x n) matrix as the adjacency matrix of a graph. It alternates an expansion step and an inflation step until an equilibrium state is reached.
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2025-09-22 |
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r-sparktf
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A 'sparklyr' extension that enables reading and writing 'TensorFlow' TFRecord files via 'Apache Spark'.
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2025-09-22 |
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r-fastverse
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Easy installation, loading and management, of a complementary set of high-performance packages for statistical computing and data manipulation. The core 'fastverse' consists of 6 packages: 'data.table', 'collapse', 'matrixStats', 'kit', 'magrittr' and 'fst', that jointly only depend on 'Rcpp'. These packages are attached and harmonized through the 'fastverse'. In addition, the 'fastverse' can be freely and permanently extended with additional packages, both globally or for individual projects. Entirely separate package verses can also be created. Selected fast and low-dependency packages are suggested for various topics such as time series, dates and times, strings, spatial data, statistics and data serialization (see GitHub / website).
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2025-09-22 |
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r-timeroc
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Estimation of time-dependent ROC curve and area under time dependent ROC curve (AUC) in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator. Plot functions for time-dependent ROC curves and AUC curves are provided. Time-dependent Positive Predictive Values (PPV) and Negative Predictive Values (NPV) can also be computed.
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2025-09-22 |
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r-ascii
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Coerce R object to asciidoc, txt2tags, restructuredText, org, textile or pandoc syntax. Package comes with a set of drivers for Sweave.
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2025-09-22 |
