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r-leapp
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public |
These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
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2025-03-25 |
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r-esabcv
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public |
These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
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2025-03-25 |
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r-bfa
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public |
Provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models under a range of priors.
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2025-03-25 |
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r-genlasso
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public |
This package computes 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 subproblems are given to improve stability and speed.
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2025-03-25 |
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r-corshrink
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public |
Performs adaptive shrinkage of correlation and covariance matrices using a mixture model prior over the Fisher z-transformation of the correlations. A separate shrinkage intensity may be specifiedfor each cell of the correlation or the covariance table.
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2025-03-25 |
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r-rcppziggurat
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public |
The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (JSS, 2000), has been improved upon a few times starting with Leong et al (JSS, 2005). This package provides an aggregation in order to compare different implementations. The goal is to provide an 'faster but good enough' alternative for use with R and C++ code.
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2025-03-25 |
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r-skmeans
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public |
Algorithms to compute spherical k-means partitions. Features several methods, including a genetic and a fixed-point algorithm and an interface to the CLUTO vcluster program.
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2025-03-25 |
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r-conicfit
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public |
Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin.
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2025-03-25 |
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r-geigen
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public |
Functions to compute generalized eigenvalues and eigenvectors, the generalized Schur decomposition and the generalized Singular Value Decomposition of a matrix pair, using Lapack routines.
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2025-03-25 |
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bioconductor-scde
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public |
The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).
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2025-03-25 |
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r-circular
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public |
Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
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2025-03-25 |
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r-ccremover
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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
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2025-03-25 |
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r-heatmap3
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public |
An improved heatmap package. Completely compatible with the original R function 'heatmap', and provides more powerful and convenient features.
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2025-03-25 |
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r-cellcycler
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public |
From gene expression data, filters out the sinusoidal genes and outputs relative times of the cells on the cell cycle.
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2025-03-25 |
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r-binhf
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public |
Binomial Haar-Fisz transforms for Gaussianization
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2025-03-25 |
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r-adlift
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public |
Adaptive wavelet lifting transforms for signal denoising using optimal local neighbourhood regression, from Nunes et al. (2006) <doi:10.1007/s11222-006-6560-y>.
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2025-03-25 |
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r-ebayesthresh
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public |
Empirical Bayes thresholding using the methods developed by I. M. Johnstone and B. W. Silverman. The basic problem is to estimate a mean vector given a vector of observations of the mean vector plus white noise, taking advantage of possible sparsity in the mean vector. Within a Bayesian formulation, the elements of the mean vector are modelled as having, independently, a distribution that is a mixture of an atom of probability at zero and a suitable heavy-tailed distribution. The mixing parameter can be estimated by a marginal maximum likelihood approach. This leads to an adaptive thresholding approach on the original data. Extensions of the basic method, in particular to wavelet thresholding, are also implemented within the package.
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2025-03-25 |
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bioconductor-flowclust
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public |
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.
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2025-03-25 |
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bioconductor-variancepartition
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public |
Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.
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2025-03-25 |
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r-gh
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public |
Minimal client to access the 'GitHub' 'API'.
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2025-03-25 |
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r-ini
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public |
Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.
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2025-03-25 |
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bismark
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public |
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
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2025-03-25 |
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r-workflowr
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public |
workflowr provides helper functions to get started using R Markdown to create a research website.
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2025-03-25 |
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bioconductor-snplocs.hsapiens.dbsnp144.grch38
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.
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2025-03-25 |
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r-ggbeeswarm
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public |
Provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.
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2025-03-25 |
