These utilities facilitate the programmatic manipulations of formulas, expressions, calls, assignments and other R language objects. These objects all share the same structure: a left-hand side, operator and right-hand side. This package provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.

a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

This package provides a fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm (SSA). This package is the spiritual successor to the GillespieSSA package. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended.

The r-und-s package decodes the german R- und S-Satze, which are numerically coded security advice for chemical substances into plain text. This is, e.g., used to compose security sheets or lab protocols and especially useful for students of chemistry. There are four packages, giving texts in German, English, French and Dutch.

The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function aba_enrich integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.

The Docker registry server enable you to host your own docker registry. With it, there is also two other utilities:

• The digest utility is a tool that generates checksums compatibles with various docker manifest files.

• The registry-api-descriptor-template is a tool for generating API specifications from the docs/spec/api.md.tmpl file.

Repeating of math operators at the broken line and the new line in inline equations is used in Cyrillic mathematical typography (Russian for example), but unfortunately LaTeX does not provide such an option. This package solves the problem by extending ideas described in M. I. Grinchuk TeX and Russian Traditions of Typesetting, and supports most of LaTeX mathematical packages.

This package extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as Latent Dirichlet Allocation (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.

Retrying is a general-purpose retrying library to simplify the task of adding retry behavior to just about anything.

Features:

• Generic Decorator API.

• Specify stop condition (i.e. limit by number of attempts).

• Specify wait condition (i.e. exponential backoff sleeping between attempts).

• Customize retrying on Exceptions.

• Customize retrying on expected returned result.

This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.

EASY-ROUTES is yet another routes handling system on top of Hunchentoot. It's just glue code for Restas routing subsystem (CL-ROUTES).

It supports:

• dispatch based on HTTP method

• arguments extraction from the url path

• decorators

• URL generation from route names

This package provides EASY-ROUTES, EASY-ROUTES+DJULA and EASY-ROUTES+ERRORS systems.

The Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

This package provides a collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package multistateQTL contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a QTLExperiment object, which is based on the SummarisedExperiment framework.

This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.

This package provides a set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques.

This Python module provides line editing functions similar to the default Emacs-style ones of GNU Readline. Unlike the Python standard library's readline package, this one allows access to those capabilities in settings outside of a standard command-line interface. It is especially well-suited to interfacing with Urwid, due to a shared syntax for describing key inputs.

Currently, all stateless Readline commands are implemented. Yanking and history are not supported.

With Serverspec, you can write RSpec tests for checking your servers are configured correctly.

Serverspec tests your servers’ actual state by executing command locally, via SSH, via WinRM, via Docker API and so on. So you don’t need to install any agent softwares on your servers and can use any configuration management tools, Puppet, Ansible, CFEngine, Itamae and so on.

But the true aim of Serverspec is to help refactoring infrastructure code.

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g. VCF, bed, wig) and other resources from standard locations (e.g. UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

The package addresses, for LaTeX documents, the severe limitation on the number of output streams that TeX provides. The package uses a single TeX output stream, and writes marked-up output to this stream. The user may then post-process the marked-up output file, using LaTeX, and the document's output appears as separate files, according to the calls made to the package. The output to be post-processed uses macros from the widely-available ProTeX package.

Ksoloti is an environment for generating and processing digital audio. It can be a programmable virtual modular synthesizer, polysynth, drone box, sequencer, chord generator, multi effect, sample player, looper, granular sampler, MIDI generator/processor, CV or trigger generator, anything in between, and more.

The Ksoloti Core is a rework of the discontinued Axoloti Core board. In short, Ksoloti aims for maximum compatibility with the original Axoloti, but with some layout changes and added features.

This package provides the runtime.