This package provides examples and code that make use of the different graph related packages produced by Bioconductor.

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

This package provides a manifest package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

This is the core package for the automated analysis of Affymetrix arrays.

Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.

Quickly find motif matches for many motifs and many sequences. This package wraps C++ code from the MOODS motif calling library.

This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.

This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

This package defines an S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

The biobtreeR package provides an interface to biobtree, a tool which covers large sets of bioinformatics datasets and allows search and chain mappings functionalities.

This package provides tools for parsing Illumina's microarray output files, including IDAT.

This package provides classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

This package provides tools to support the analysis of RNA-seq expression data or other similar kind of data. It provides exploratory plots to evaluate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. It also supports the analysis of differential expression between two experimental conditions with no parametric assumptions.

This package provides a collection of compression filters for use with HDF5 datasets.

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

The package ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be transformed into expression data matrix. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A graphical user interface (GUI) is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

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

The aim of TCGAbiolinks is:

1. facilitate GDC open-access data retrieval;

2. prepare the data using the appropriate pre-processing strategies;

3. provide the means to carry out different standard analyses, and;

4. to easily reproduce earlier research results.

In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

The affyPLM provides a package that extends and improves the functionality of the base affy package. For speeding up the runs, it includes routines that make heavy use of compiled code. The central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools are also provided.

This package provides functions and classes for de novo prediction of transcription factor binding consensus by heuristic search.

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

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang, respectively, for measuring semantic similarities among Disease ontology (DO) terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.