Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.

This package provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

This package contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A graphical display of large correlation matrices, The American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.

This package implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.

This package provides a regular expression toolkit for regex-base with compile-time checking of regular expression syntax, data types for matches and captures, a text replacement toolkit, portable options, high-level AWK-like tools for building text processing apps, regular expression macros with parsers and test bench, comprehensive documentation, tutorials and copious examples.

The 6581 SID chip is the sound chip used in the Commodore 64 computer. reMID is a MIDI implementation of the 6581 SID chip using the reSID library to provide a virtual SID-based synthesizer, controllable in real-time via MIDI. It includes support for scripted instruments that allow complex sonic control of the chip.

BiocSet displays different biological sets in a triple tibble format. These three tibbles are element, set, and elementset. The user has the ability to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.

This is a package for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. It provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. It includes GRanges generation and plotting functions.

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

This package provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.

Stringr is a consistent, simple and easy to use set of wrappers around the fantastic stringi package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

To make it easy to create CONSORT diagrams for the transparent reporting of participant allocation in randomized, controlled clinical trials. This is done by creating a standardized disposition data, and using this data as the source for the creation a standard CONSORT diagram. Human effort by supplying text labels on the node can also be achieved.

r-selectr translates a CSS3 selector into an equivalent XPath expression. This allows you to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package cssselect.

ibus-rime provides the Rime input method engine for IBus. Rime is a lightweight, extensible input method engine supporting various input schemas including glyph-based input methods, romanization-based input methods as well as those for Chinese dialects. It has the ability to compose phrases and sentences intelligently and provide very accurate traditional Chinese output.

metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.

The r-nleqslv package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.

This package provides a data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

Sending functions to remote processes can be wasteful of resources because they carry their environments with them. With this package, it is easy to create functions that are isolated from their environment. These isolated functions, also called crates, print to the console with their total size and can be easily tested locally before being sent to a remote.

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

This package provides a single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

This package provides various themes, palettes, and other functions that are used to customise ggplots to look like they were made in GraphPad Prism. The Prism-look is achieved with theme_prism() and scale_fill|colour_prism(), axes can be changed with custom guides like guide_prism_minor(), and significance indicators added with add_pvalue().

This package 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, where it is used 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.