This package stores all schemas required by various alabaster.* packages. No computation should be performed by this package, as that is handled by alabaster.base.

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package.

This package performs multiple co-inertia analysis of omics datasets.

Microarray quality assessment is a major concern of microarray analysts. This package provides some simple approaches to in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics.

systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.

This package provides an R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualization tools. Besides providing an easy to use set of tools for manipulating the data from BaseSpace, it also facilitates the access to R's rich environment of statistical and data analysis tools.

This package provides a set of protein ID mappings for PFAM, assembled using data from public repositories.

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

This package provides tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

This package provides UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.

This package provides methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via DTU (differential transcript usage), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via MCMC (Markov chain Monte Carlo) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.

This package provides utilities for flow cytometry data.

This package provides methods for working with Illumina arrays using the gdsfmt package.

This is a package for saving Bioconductor data structures into file artifacts, and loading them back into memory. This is a more robust and 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.

Data package for JASPAR2020. To explore these databases, utilize the TFBSTools package (version 1.23.1 or higher).

Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version hs37d5.

This package provides genome wide annotations for Bovine, primarily based on mapping using Entrez Gene identifiers.

This package provides a simple interface to and data from the Human Protein Atlas project.

This is an annotation package for Illumina's EPIC methylation arrays.

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg38 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

This package provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

This package provides an R interface to Megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files.

This package provides utilities for Receiver Operating Characteristic (ROC) curves, with a focus on micro arrays.