This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation.

Graphite provides networks derived from eight public pathway databases, and automates the conversion of node identifiers (e.g. from Entrez IDs to gene symbols).

This package provides Affymetrix HG-U133A Array annotation data (chip hgu133a) assembled using data from public repositories.

This package is an implementation of the Adaptively Weighted Fisher's method, including fast p-value computing, variability index, and meta-pattern.

This package allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

This package implements sampling, iteration, and input of FASTQ files. It includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

This package contains example data for Illumina microarray output files, for testing purposes.

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus.

This package provides the complete genome sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top:

1. the mask of assembly gaps (AGAPS mask);

2. the mask of intra-contig ambiguities (AMB mask);

3. the mask of repeats from RepeatMasker (RM mask);

4. the mask of repeats from Tandem Repeats Finder (TRF mask).

Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.

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

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

This package translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

This is a package for identification of metabolites using high precision mass spectrometry. MS peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.

This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.

This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

This package lets you carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. It implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data like gene expression/RNA sequencing/methylation/brain imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.

The AffiXcan package imputes a genetically regulated expression (GReX) for a set of genes in a sample of individuals, using a method based on the total binding affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.

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 provides tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.