|
r-clustassess
|
public |
A set of tools for evaluating clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), as well as similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables stability-based parameter assessment for graph-based clustering pipelines typical in single-cell data analysis.
|
2025-09-24 |
|
r-fourpno
|
public |
Estimate Barton & Lord's (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x> four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477-6>.
|
2025-09-24 |
|
adios-db
|
public |
Package for working with data in the NOAA ADIOS Oil Database
|
2025-09-24 |
|
adios_db
|
public |
Package for working with data in the NOAA ADIOS Oil Database
|
2025-09-24 |
|
r-bigalgebra
|
public |
Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
|
2025-09-24 |
|
r-treeman
|
public |
S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
|
2025-09-24 |
|
r-netmeta
|
public |
A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis": - frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>; - net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>; - measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>; - ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>; - partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>; - split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>; - league table with network meta-analysis results; - additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <DOI:10.1002/bimj.201800167>; - network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>; - 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>; - automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>; - rankograms and ranking by SUCRA; - contribution matrix as described in Papakonstantinou et al. (2018) <DOI:10.12688/f1000research.14770.3> and Davies et al. (2021) <arXiv:2107.02886>.
|
2025-09-24 |
|
r-workflowr
|
public |
Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.
|
2025-09-24 |
|
r-rferns
|
public |
Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.
|
2025-09-24 |
|
r-qdap
|
public |
Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.
|
2025-09-24 |
|
r-shinymatrix
|
public |
Implements a custom matrix input field.
|
2025-09-24 |
|
r-glpkapi
|
public |
R Interface to C API of GLPK, depends on GLPK Version >= 4.42.
|
2025-09-24 |
|
r-genlasso
|
public |
Provides fast algorithms for computing the solution path for generalized lasso problems. Important use cases are the fused lasso over an arbitrary graph, and trend fitting of any given polynomial order. Specialized implementations for the latter two problems are given to improve stability and speed.
|
2025-09-24 |
|
r-ggconf
|
public |
A flexible interface for ggplot2::theme(), potentially saving 50% of your typing.
|
2025-09-24 |
|
r-plackettluce
|
public |
Functions to prepare rankings data and fit the Plackett-Luce model jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce (1959, ISBN:0486441369). The standard Plackett-Luce model is generalized to accommodate ties of any order in the ranking. Partial rankings, in which only a subset of items are ranked in each ranking, are also accommodated in the implementation. Disconnected/weakly connected networks implied by the rankings may be handled by adding pseudo-rankings with a hypothetical item. Optionally, a multivariate normal prior may be set on the log-worth parameters and ranker reliabilities may be incorporated as proposed by Raman and Joachims (2014) <doi:10.1145/2623330.2623654>. Maximum a posteriori estimation is used when priors are set. Methods are provided to estimate standard errors or quasi-standard errors for inference as well as to fit Plackett-Luce trees. See the package website or vignette for further details.
|
2025-09-24 |
|
tiledb
|
public |
TileDB sparse and dense multi-dimensional array data management
|
2025-09-24 |
|
mastodon.py
|
public |
Python wrapper for the Mastodon API
|
2025-09-24 |
|
r-hdci
|
public |
Fits regression models on high dimensional data to estimate coefficients and use bootstrap method to obtain confidence intervals. Choices for regression models are Lasso, Lasso+OLS, Lasso partial ridge, Lasso+OLS partial ridge.
|
2025-09-24 |
|
r-utility
|
public |
Construct and plot objective hierarchies and associated value and utility functions. Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables. Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies. Get numerical results of the evaluations in standard R data types for further processing.
|
2025-09-24 |
|
r-dendroextras
|
public |
Provides extra functions to manipulate dendrograms that build on the base functions provided by the 'stats' package. The main functionality it is designed to add is the ability to colour all the edges in an object of class 'dendrogram' according to cluster membership i.e. each subtree is coloured, not just the terminal leaves. In addition it provides some utility functions to cut 'dendrogram' and 'hclust' objects and to set/get labels.
|
2025-09-24 |
|
r-rmsnumpress
|
public |
'Rcpp' bindings to the native C++ implementation of MS Numpress, that provides two compression schemes for numeric data from mass spectrometers. The library provides implementations of 3 different algorithms, 1 designed to compress first order smooth data like retention time or M/Z arrays, and 2 for compressing non smooth data with lower requirements on precision like ion count arrays. Refer to the publication (Teleman et al., (2014) <doi:10.1074/mcp.O114.037879>) for more details.
|
2025-09-24 |
|
r-repo
|
public |
A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with rich annotations, including corresponding code chunks, and easily searched and retrieved.
|
2025-09-24 |
|
r-diagrammer
|
public |
Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.
|
2025-09-24 |
|
r-bio3d
|
public |
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
|
2025-09-24 |
|
r-extrafont
|
public |
Tools to using fonts other than the standard PostScript fonts. This package makes it easy to use system TrueType fonts and with PDF or PostScript output files, and with bitmap output files in Windows. extrafont can also be used with fonts packaged specifically to be used with, such as the fontcm package, which has Computer Modern PostScript fonts with math symbols. See https://github.com/wch/extrafont for instructions and examples.
|
2025-09-24 |
