Bioconductor v3.9.0 API Reference

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

The package contains functions for exploratory

A package that extends and improves the functionality of

Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.

Using R enviroments for annotation.

Implements a user-friendly interface for querying SQLite-based annotation data packages.

This package provides class and other infrastructure to

Provides code for generating Annotation packages and

This package provides a client for the Bioconductor

Infrastructure shared by all the Biostrings-based genome data

Provides a consistent C++ class interface for reading from and

Functions that are needed by many other packages or which

The package defines S4 generic functions used in Bioconductor.

This package is used to install and update Bioconductor,

This package provides modified versions and novel

Provides standard formatting styles for Bioconductor PDF

This package provides repository information for the appropriate

Infrastructure to support 'views' used to classify

In recent years a wealth of biological data has become available

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and

Memory efficient string containers, string matching

The biovizBase package is designed to provide a set of

Tools for finding bumps in genomic data

A collection of tools for performing category (gene set

This package implements methods to analyze and visualize

Complex heatmaps are efficient to visualize associations

algorithm for determining cluster count and membership by

Estimate variance-mean dependence in count data from

Estimate variance-mean dependence in count data from

Implements the circular binary segmentation (CBS)

This package implements five methods proposed by

Wrapping an array-like object (typically an on-disk object) in

A port of the 'matrixStats' API for use with DelayedMatrix objects

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Numerical and graphical summaries of RNA-Seq read data.

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.

The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis.

The package provides functions to create and use

The package implements an algorithm for fast gene set enrichment

Provides S4 data structures and basic functions to deal with flow

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

The semantic comparisons of Gene Ontology (GO) annotations provide

A set of tools for interacting with GO and microarray

This package provides classes and methods to support Gene

Background adjustment using sequence information

Some basic functions for filtering genes.

Functions for plotting genomic data

Contains data and functions that

Provides efficient containers for storing and manipulating

A set of tools and methods for making and manipulating

The ability to efficiently represent and manipulate genomic

The ggbio package extends and specializes the grammar of

'ggtree' extends the 'ggplot2' plotting system which implemented

A package that implements some simple graph handling

Genomic data analyses requires integrated visualization

Implements the HDF5Array and TENxMatrix classes, 2 convenient

Provides efficient low-level and highly reusable S4

Tools for parsing Illumina's microarray output files, including IDAT.

Imputation for microarray data (currently KNN only)

The interactiveDisplayBase package contains the the basic

A package that provides a client interface to the KEGG

KEGGGraph is an interface between KEGG pathway and graph

Data analysis, linear models and differential expression for microarray data.

MSnbase provides infrastructure for manipulation,

Class definitions for two-color spotted microarray data.

Tools to analyze & visualize Illumina Infinium methylation arrays.

Monocle performs differential expression and time-series analysis

Non-parametric bootstrap and permutation resampling-based

mzR provides a unified API to the common file formats and

A package to analyze oligonucleotide arrays

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

The package enables a simple unified interface to several

Pathview is a tool set for pathway based data integration

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA,

phyloseq provides a set of classes and tools

A library of core preprocessing routines.

S4 generic functions needed by Bioconductor proteomics

This package takes a list of p-values resulting from the

A fairly extensive and comprehensive interface to the

Interfaces R with the AT and T graphviz library for

This package provides an interface between HDF5 and R.

Provides C and C++ hdf5 libraries.

This package provides an interface to the 'samtools',

Extensible framework for interacting with multiple genome

The S4Vectors package defines the Vector and List virtual classes

A collection of tools for doing various analyses of

This package implements sampling, iteration, and input of

Identification of differentially expressed genes and

Defines a S4 class for storing data from single-cell

The SummarizedExperiment container contains one or more assays,

The sva package contains functions for removing batch

The aim of TCGAbiolinks is : i) facilitate the GDC open-access

topGO package provides tools for testing GO terms while

Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file.

Imports transcript-level abundance, estimated counts and

Annotate variants, compute amino acid coding changes,

The package implements a method for normalising microarray intensities, and works

Provides memory efficient S4 classes for storing sequences

This package uses the source code of zlib-1.2.5 to create