This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The epivizrServer package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.

Snapbox is a snapshot-testing toolbox that is ready to use for verifying output from

• Function return values

• CLI stdout/stderr

• Filesystem changes

It is also flexible enough to build your own test harness like trycmd.

Snapbox is a snapshot-testing toolbox that is ready to use for verifying output from

• Function return values

• CLI stdout/stderr

• Filesystem changes

It is also flexible enough to build your own test harness like trycmd.

Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance.

Computation and visualization of matrix correlation coefficients. The main method is the Similarity of Matrices Index, while various related measures like r1, r2, r3, r4, Yanai's GCD, RV, RV2, adjusted RV, Rozeboom's linear correlation and Coxhead's coefficient are included for comparison and flexibility.

This package provides a tm Source to create corpora from a corpus prepared in the format used by the Alceste application (i.e. a single text file with inline meta-data). It is able to import both text contents and meta-data (starred) variables.

This package provides a developer-facing interface to Arrow Database Connectivity (ADBC) for the purposes of driver development, driver testing, and building high-level database interfaces for users. ADBC is an API standard for database access libraries that uses Arrow for result sets and query parameters.

Third parties often change the page numbers without rerunning makeindex. One would like to make the page numbers in the index entries more robust. This bundle provides robustindex.sty and robustglossary.sty, which use the \pageref mechanism to maintain correct page numbers.

parinfer-rust-emacs is an Emacs-centric fork of parinfer-rust, itself an implementation of Shaun Lebron’s Parinfer. This builds a shared library intended to be loaded by the emacs-parinfer-rust-mode Emacs plugin, though a standalone binary is built also.

This package provides classes and methods that allow the user to manage life table, actuarial tables (also multiple decrements tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.

This package provides functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from MALDIquant objects.

The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012).

Provides functions which facilitate writing multi-file Emacs packages and running from the source tree without having to "install" code or fiddle with load-path.

The main function, load-relative, loads an Emacs Lisp file relative to another (presumably currently running) Emacs Lisp file.

repl-utilities is a set of utilities which ease life at the REPL. It includes three sorts of features: introspective procedures, miscellaneous utility functions, and, pulling them together, methods to conveniently keep these symbols and optionally additional symbols available in whichever package you switch to.

This package provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included.

runewidth provides functions to get fixed width of the character or string. It is a fork of https://github.com/mattn/go-runewidth, updated to the newest Unicode and having various helper functions removed, so all that remains is just the runewidth.RuneWidth() function.

The Read activity allows the laptop to act as a book reader. It has a simple interface, and will view many kinds of text and image-based book-like materials. It will have particular strengths in handheld mode, with extremely low power consumption and simple navigation controls.

This package provides SPSS- and SAS-like output for least squares multiple regression, logistic regression, and count variable regressions. Detailed output is also provided for OLS moderated regression, interaction plots, and Johnson-Neyman regions of significance. The output includes standardized coefficients, partial and semi-partial correlations, collinearity diagnostics, plots of residuals, and detailed information about simple slopes for interactions. The output for some functions includes Bayes Factors and, if requested, regression coefficients from Bayesian Markov Chain Monte Carlo analyses. There are numerous options for model plots. The REGIONS_OF_SIGNIFICANCE function also provides Johnson-Neyman regions of significance and plots of interactions for both lm and lme models.

General matrix multiplication for f32 and f64 matrices. Operates on matrices with general layout (they can use arbitrary row and column stride). Detects and uses AVX or SSE2 on x86 platforms transparently for higher performance. Uses a microkernel strategy, so that the implementation is easy to parallelize and optimize.

General matrix multiplication for f32 and f64 matrices. Operates on matrices with general layout (they can use arbitrary row and column stride). Detects and uses AVX or SSE2 on x86 platforms transparently for higher performance. Uses a microkernel strategy, so that the implementation is easy to parallelize and optimize.

General matrix multiplication for f32 and f64 matrices. Operates on matrices with general layout (they can use arbitrary row and column stride). Detects and uses AVX or SSE2 on x86 platforms transparently for higher performance. Uses a microkernel strategy, so that the implementation is easy to parallelize and optimize.

Simple, fast, and automatic encodings for category data using a data.table backend. Most of the methods are an implementation of "Sufficient Representation for Categorical Variables" by Johannemann, Hadad, Athey, Wager (2019) <arXiv:1908.09874>, particularly their mean, sparse principal component analysis, low rank representation, and multinomial logit encodings.

Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Bio-commandeer provides an opinionated method of running shell commands from within Ruby. The advantage of bio-commandeer over other methods of running external commands is that when something goes wrong, messages printed to the STDOUT and STDERR streams are reported, giving extra detail to ease debugging.