BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

Org-Roam-UI is a frontend for exploring and interacting with your org-roam notes.

Org-Roam-UI is meant a successor of org-roam-server that extends functionality of org-roam with a Web app that runs side-by-side with Emacs.

This package provides a udev rules file that allows unprivileged users communication with the Teensy family of micro-controllers. ModemManager (part of NetworkManager) can interfere with USB Serial devices, which includes the Teensy. In case of problems, see the .rules file for possible workarounds.

Click is a "Python package for creating beautiful command line interfaces". Rich is a "Python library for rich text and beautiful formatting in the terminal". The intention of rich-click is to provide attractive help output from click, formatted with rich, with minimal customization required.

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.

Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS.

Markup allows the use of HTML syntax with in Common Lisp code. This has the advantage of being able to copy HTML snippets and have them instantly be functional, less double quotes than a s-expression approach, and designers will be able to understand the embedded HTML.

HTMLProofer is a set of tests to validate your HTML output. These tests check if your image references are legitimate, if they have alt tags, if your internal links are working, and so on. It's intended to be an all-in-one checker for your output.

This package allows the user to input formatted data into elements of a 2-D or 3-D array and to recall that data at will by individual cell number. The data can be but need not be numerical in nature. It can be, for example, formatted text.

This package runs R-code present in a pandoc markdown file and includes the resulting output in the resulting markdown file. This file can then be converted into any of the output formats supported by pandoc. The package can also be used as an engine for writing package vignettes.

The package uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

Libretro is a simple but powerful development interface that allows for the easy creation of emulators, games and multimedia applications that can plug straight into any libretro-compatible frontend. RetroArch is the official reference frontend for the libretro API, currently used by most as a modular multi-system game/emulator system.

This package provides a Tryton module for assigning roles to user instead of groups. A Role is defined by a set of groups. When a role is added to a user, it overrides the existing groups. A role can be added to a user for a period of time only.

This package provides a gem to convert LaTeX input to Unicode. Its original use was as an input filter for BibTeX-Ruby, but it can be used independently to decode LaTeX. Many of the patterns used by this Ruby gem are based on François Charette's equivalent Perl module LaTeX::Decode.

The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.

r-circrnaprofiler is a computational framework for a comprehensive in silico analysis of circular RNA (circRNAs). This computational framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., acosh', log(x+1)'), (2) model residual based (Pearson and randomized quantile residuals).

This module, ReadKey, provides ioctl control for terminals so the input modes can be changed (thus allowing reads of a single character at a time), and also provides non-blocking reads of stdin, as well as several other terminal related features, including retrieval/modification of the screen size, and retrieval/modification of the control characters.

This package provides a toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.

This package detects naive associations between omics features and metadata in cross-sectional data-sets using non-parametric tests. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests. The generated output can be graphically summarized using the built-in plotting function.

This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.

Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data.

This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.

This package provides tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction.