|
r-cgh
|
public |
Functions to analyze microarray comparative genome hybridization data using the Smith-Waterman algorithm
|
2025-04-22 |
|
r-cggp
|
public |
Run computer experiments using the adaptive composite grid algorithm with a Gaussian process model. The algorithm works best when running an experiment that can evaluate thousands of points from a deterministic computer simulation. This package is an implementation of a forthcoming paper by Plumlee, Erickson, Ankenman, et al. For a preprint of the paper, contact the maintainer of this package.
|
2025-04-22 |
|
r-bsts
|
public |
Time series regression using dynamic linear models fit using MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many other sources.
|
2025-04-22 |
|
r-bigtabulate
|
public |
Extend the bigmemory package with 'table', 'tapply', and 'split' support for 'big.matrix' objects. The functions may also be used with native R matrices for improving speed and memory-efficiency.
|
2025-04-22 |
|
r-adjclust
|
public |
Implements a constrained version of hierarchical agglomerative clustering, in which each observation is associated to a position, and only adjacent clusters can be merged. Typical application fields in bioinformatics include Genome-Wide Association Studies or Hi-C data analysis, where the similarity between items is a decreasing function of their genomic distance. Taking advantage of this feature, the implemented algorithm is time and memory efficient. This algorithm is described in Chapter 4 of Alia Dehman (2015) <https://hal.archives-ouvertes.fr/tel-01288568v1>.
|
2025-04-22 |
|
r-cgdsr
|
public |
Provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC) at <www.cbioportal.org>.
|
2025-04-22 |
|
r-cfma
|
public |
Performs causal functional mediation analysis (CFMA) for functional treatment, functional mediator, and functional outcome. This package includes two functional mediation model types: (1) a concurrent mediation model and (2) a historical influence mediation model. See Zhao et al. (2018), Functional Mediation Analysis with an Application to Functional Magnetic Resonance Imaging Data, <arXiv:1805.06923> for details.
|
2025-04-22 |
|
r-cfestimatequantiles
|
public |
Estimate quantiles using formula (18) from http://www.jaschke-net.de/papers/CoFi.pdf (Yaschke; 2001)
|
2025-04-22 |
|
r-cetcolor
|
public |
Collection of perceptually uniform colour maps made by Peter Kovesi (2015) "Good Colour Maps: How to Design Them" <arXiv:1509.03700> at the Centre for Exploration Targeting (CET).
|
2025-04-22 |
|
r-cernn
|
public |
An implementation of the covariance estimation method proposed in Chi and Lange (2014), "Stable estimation of a covariance matrix guided by nuclear norm penalties," Computational Statistics and Data Analysis 80:117-128.
|
2025-04-22 |
|
r-cernaseek
|
public |
Provides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, For predictive ceRNA relationship pairs, this package provides several downstream analysis algorithms, including regulatory network analysis and functional annotation analysis, as well as survival prognosis analysis based on expression of ceRNA ternary pair.
|
2025-04-22 |
|
r-ceriolioutlierdetection
|
public |
Implements the iterated RMCD method of Cerioli (2010) for multivariate outlier detection via robust Mahalanobis distances. Also provides the finite-sample RMCD method discussed in the paper, as well as the methods provided in Hardin and Rocke (2005) <doi:10.1198/106186005X77685> and Green and Martin (2017).
|
2025-04-22 |
|
r-centiserve
|
public |
Calculates centrality indices additional to the 'igraph' package centrality functions.
|
2025-04-22 |
|
r-censys
|
public |
The 'Censys' public search engine enables researchers to quickly ask questions about the hosts and networks that compose the Internet. Details on how 'Censys' was designed and how it is operated are available at <https://www.censys.io/about>. Both basic and extended research access queries are made available. More information on the SQL dialect used by the 'Censys' engine can be found at <https://cloud.google.com/bigquery/docs/reference/legacy-sql>.
|
2025-04-22 |
|
r-censusapi
|
public |
A wrapper for the U.S. Census Bureau APIs that returns data frames of Census data and metadata. Available datasets include the Decennial Census, American Community Survey, Small Area Health Insurance Estimates, Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
|
2025-04-22 |
|
r-census2016
|
public |
Contains selected variables from the time series profiles for statistical areas level 2 from the 2006, 2011, and 2016 censuses of population and housing, Australia. Also provides methods for viewing the questions asked for convenience during analysis.
|
2025-04-22 |
|
r-censregmod
|
public |
Fits univariate censored linear regression model under Normal or Student-t distribution
|
2025-04-22 |
|
r-censorcopula
|
public |
Implement an interval censor method to break ties when using data with ties to fitting a bivariate copula.
|
2025-04-22 |
|
r-censcov
|
public |
Implementations of threshold regression approaches for linear regression models with a covariate subject to random censoring, including deletion threshold regression and completion threshold regression. Reverse survival regression, which flip the role of response variable and the covariate, is also considered.
|
2025-04-22 |
|
r-cengam
|
public |
Implementation of Tobit type I and type II families for censored regression using the 'mgcv' package, based on methods detailed in Woods (2016) <doi:10.1080/01621459.2016.1180986>.
|
2025-04-22 |
|
r-cdrom
|
public |
Classification is based on the recently developed phylogenetic approach by Assis and Bachtrog (2013). The method classifies the evolutionary mechanisms retaining pairs of duplicate genes (conservation, neofunctionalization, subfunctionalization, or specialization) by comparing gene expression profiles of duplicate genes in one species to those of their single- copy ancestral genes in a sister species.
|
2025-04-22 |
|
r-cdnmoney
|
public |
Components of Canadian Credit Aggregates and Monetary Aggregates with continuity adjustments.
|
2025-04-22 |
|
r-cdft
|
public |
This package proposes a statistical downscaling method for cumulative distribution functions (CDF), as well as the computation of the Cram\`er-von Mises statistics U, and the Kolmogorov-Smirnov statistics KS.
|
2025-04-22 |
|
r-cdb
|
public |
A constant database is a data structure created by Daniel J. Bernstein in his cdb package. Its format consists on a sequence of (key,value)-pairs. This R package replicates the basic utilities for reading (cdbget) and writing (cdbdump) constant databases.
|
2025-04-22 |
|
r-ccremover
|
public |
Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.
|
2025-04-22 |
