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r-tractor.base
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public |
Functions for working with magnetic resonance images. Reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualisation; flexible image manipulation; metadata and sparse image handling.
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2025-04-22 |
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r-maldiquant
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public |
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
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2025-04-22 |
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r-laplacesdemon
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public |
Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.
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2025-04-22 |
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r-colourpicker
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A colour picker that can be used as an input in Shiny apps or Rmarkdown documents. The colour picker supports alpha opacity, custom colour palettes, and many more options. A Plot Colour Helper tool is available as an RStudio Addin, which helps you pick colours to use in your plots. A more generic Colour Picker RStudio Addin is also provided to let you select colours to use in your R code.
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2025-04-22 |
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r-smoothmest
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Some M-estimators for 1-dimensional location (Bisquare, ML for the Cauchy distribution, and the estimators from application of the smoothing principle introduced in Hampel, Hennig and Ronchetti (2011) to the above, the Huber M-estimator, and the median, main function is smoothm), and Pitman estimator.
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2025-04-22 |
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r-sm
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This is software linked to the book 'Applied Smoothing Techniques for Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University Press.
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2025-04-22 |
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r-rcircos
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A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
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2025-04-22 |
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r-ccremover
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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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2025-04-22 |
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r-log4r
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public |
The log4r package is meant to provide a fast, lightweight, object-oriented approach to logging in R based on the widely-emulated 'log4j' system and etymology.
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2025-04-22 |
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r-tfmpvalue
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In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007) <DOI:10.1186/1748-7188-2-15>.
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2025-04-22 |
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r-liblinear
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public |
A wrapper around the LIBLINEAR C/C++ library for machine learning.
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2025-04-22 |
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r-readmzxmldata
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public |
Functions for reading mass spectrometry data in mzXML format.
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2025-04-22 |
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r-glasso
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public |
Estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.
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2025-04-22 |
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r-readbrukerflexdata
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Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series.
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2025-04-22 |
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r-rda
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Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.
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2025-04-22 |
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r-protviz
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public |
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
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2025-04-22 |
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r-matrixeqtl
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Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.
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2025-04-22 |
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r-seqinr
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public |
Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 <doi:10.1093/nar/12.1Part1.121>.
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2025-04-22 |
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r-rphylip
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Rphylip provides an R interface for the PHYLIP package. All users of Rphylip will thus first have to install the PHYLIP phylogeny methods program package (Felsenstein 2013). See http://www.phylip.com for more information about installing PHYLIP.
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2025-04-22 |
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r-mrmre
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Computes mutual information matrices from continuous, categorical and survival variables, as well as feature selection with minimum redundancy, maximum relevance (mRMR) and a new ensemble mRMR technique.
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2025-04-22 |
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r-haplo.stats
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Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are
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2025-04-22 |
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r-gwidgets
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gWidgets provides a toolkit-independent API for building interactive GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project http
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2025-04-22 |
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r-dynamictreecut
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Contains methods for detection of clusters in hierarchical clustering dendrograms.
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2025-04-22 |
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r-desolve
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Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.
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2025-04-22 |
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r-rcppannoy
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'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
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2025-04-22 |
