An all-in-one document reader for GNU Emacs, supporting all major document formats. This package intends to take from doc-view, nov.el, and pdf-tools and make them better. And as such, it is effectively a drop-in replacement for them.

This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018.

This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank single value decompositions (SVDs) on large sparse centered matrices (i.e. principal components).

The R package data.table is an extension of data.frame providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.

The ggcorrplot package can be used to visualize easily a correlation matrix using ggplot2. It provides a solution for reordering the correlation matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.

This package adds custom processing for warnings for Ruby, including the ability to ignore specific warning messages, ignore warnings in specific files/directories, include backtraces with warnings, treat warnings as errors, deduplicate warnings, and add custom handling for all warnings in specific files/directories.

This package implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.

This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package.

This collection of utilities contains tooling and templates to assist in creating releases on GitHub and publishing them on PyPI. It is designed to be used by Robot Framework and tools and libraries in its ecosystem, but can naturally be used also by other projects.

This package provides an mlr3 extension that provides various resampling-based confidence interval (CI) methods for estimating the generalization error. These CI methods are implemented as mlr3 measures, enabling the evaluation of individual algorithms on specific tasks as well as the comparison of different learning algorithms.

This package provides a variety of descriptive multivariate analyses with the singular value decomposition, such as principal components analysis, correspondence analysis, and multidimensional scaling. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.

Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages.

This class implements the File Transfer Protocol. If you have used a command-line FTP program, and are familiar with the commands, you will be able to use this class easily. Some extra features are included to take advantage of Ruby's style and strengths.

The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

This package provides utilities to understand and describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion such as Highest Density Interval (HDI), and indices used for null-hypothesis testing (such as ROPE percentage and pd).

Rachana is a Malayalam font designed by Hussain K H. The project was part of Rachana Aksharavedi for the original script of Malayalam in computing. Rachana has about 1,200+ glyphs for Malayalam and contains glyphs required for printing old Malayalam books without compromising the writing style.

cl-rmath is a simple, autogenerated foreign interface for the standalone R API libRmath. There has been no effort to provide a high-level interface for the original library, instead, this library is meant to serve as a building block for such an interface.

Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19.

ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.

This package provides a Poisson mixture model is implemented to cluster genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

Radon is a Python tool which computes various code metrics. Supported metrics are:

• raw metrics: SLOC, comment lines, blank lines, &c.

• Cyclomatic Complexity (i.e., McCabe’s Complexity)

• Halstead metrics (all of them)

• the Maintainability Index (a Visual Studio metric)

This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures.

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.