Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.

This package provides an implementation of the RDF4J Rio API, which reads and writes XML.

This package provides an implementation of the RDF4J Rio API, which reads and writes Turtle.

This package provides an implementation of the RDF4J Rio API, which reads and writes NQuads.

This package provides an implementation of the RDF4J Rio API, which reads and writes JSON-LD.

This package provides a method to decompose a univariate time series into meaningful subcomponents for analysis and denoising.

CatalystX::RoleApplicator applies roles to Catalyst application classes.

Documentation at https://melpa.org/#/repl-driven-development

This package provides support for the Eclipse extension registry.

Documentation at https://melpa.org/#/find-file-in-repository

This package implements a fake S3 server for rclone.

Regexp2 is a feature-rich RegExp engine for Go.

Redigo is a Go client for the Redis database.

This package provides utilities for Google Media Downloads and Resumable Uploads.

Regexp2 is a feature-rich RegExp engine for Go.

Package router is a trie based high performance HTTP request router.

This package implements a functionality to read project dependencies from requirements.txt.

This package provides a Language Server Protocol (LSP) development kit for Ruby.

Package ring implements a FIFO queue backed by a ring buffer.

Readline is a pure Go implementation of a GNU-Readline like library.

This package contains a transport implementation based on files, for use in Maven.