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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
r-binhf
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public |
Binomial Haar-Fisz transforms for Gaussianization
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2025-03-25 |
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 |
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 |
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 |
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 |
r-gh
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public |
Minimal client to access the 'GitHub' 'API'.
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2025-03-25 |
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 |
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 |
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 |
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 |
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 |
r-beeswarm
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public |
The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.
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2025-03-25 |
r-vipor
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public |
Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
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2025-03-25 |
r-covr
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public |
Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' (http://codecov.io) or 'Coveralls' (http://coveralls.io). Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
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2025-03-25 |
r-ashr
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public |
The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <DOI:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users.
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2025-03-25 |
r-etrunct
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public |
Computes moments of univariate truncated t distribution. There is only one exported function, e_trunct(), which should be seen for details.
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2025-03-25 |
r-squarem
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public |
Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("SQUAREM").
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2025-03-25 |