BioConductor 中の bioinformatics 関連パッケージ

ソース BioConductor

これもR FAQからのネタですが、CRAN以外にbioinfomatics関連のパッケージです。 (将来はCRANに入るそうですが、、、)

Add-on packages from BioConductor The Bioconductor Project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays. The following R packages are contained in the current release of BioConductor, with more packages under development.

AnnBuilder Assemble and process genomic annotation data, from databases such as GenBank, the Gene Ontology Consortium, LocusLink, UniGene, the UCSC Human Genome Project.

Biobase Object-oriented representation and manipulation of genomic data (S4 class structure).

DynDoc Functionality to create and interact with dynamic documents, vignettes, and other navigable documents.

RBGL An interface between the graph package and the Boost graph libraries, allowing for fast manipulation of graph objects in R.

ROC Receiver Operating Characteristic (ROC) approach for identifying genes that are differentially expressed in two types of samples.

Rgraphviz An interface with Graphviz for plotting graph objects in R.

Ruuid Creates Universally Unique ID values (UUIDs) in R.

SAGElyzer Locates genes based on SAGE tags.

affy Methods for Affymetrix Oligonucleotide Arrays.

affycomp Graphics toolbox for assessment of Affymetrix expression measures.

affydata Affymetrix data for demonstration purposes.

annotate Associate experimental data in real time to biological metadata from web databases such as GenBank, LocusLink and PubMed. Process and store query results. Generate HTML reports of analyses.

edd Expression density diagnostics: graphical methods and pattern recognition algorithms for distribution shape classification.

genefilter Tools for sequentially filtering genes using a wide variety of filtering functions. Example of filters include: number of missing value, coefficient of variation of expression measures, ANOVA p-value, Cox model p-values. Sequential application of filtering functions to genes.

geneplotter Graphical tools for genomic data, for example for plotting expression data along a chromosome or producing color images of expression data matrices.

graph Classes and tools for creating and manipulating graphs within R.

hexbin Binning functions, in particular hexagonal bins for graphing.

limma Linear models for microarray data.

marrayClasses Class definitions for pre-normalized and normalized cDNA microarray data. Basic methods for accessing/replacing, printing, and subsetting.

marrayInput Functions for reading microarray data into R from different image analysis output files, and probe and target description files. Widgets are supplied to facilitate and automate data input and the creation of microarray specific R objects for storing these data.

marrayNorm Functions for location and scale normalization procedures based on robust local regression.

marrayPlots Functions for diagnostic plots for pre- and post-normalization cDNA microarray intensity data: boxplots, scatter-plots, color images.

marrayTools Miscellaneous functions used in the functional genomics core facility in UCB and UCSF.

multtest Multiple testing procedures for controlling the family-wise error rate (FWER) and the false discovery rate (FDR). Tests can be based on t- or F-statistics for one- and two-factor designs, and permutation procedures are available to estimate adjusted p-values.

reposTools Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files.

rhdf5 Storage and retrieval of large datasets using the HDF5 library and file format.

tkWidgets Widgets in Tcl/Tk that provide functionality for Bioconductor packages.

vsn Calibration and variance stabilizing transformations for both Affymetrix and cDNA array data.

widgetTools Tools for creating Tcl/Tk widgets, i.e., small-scale graphical user interfaces. These packages will eventually also be made available via CRAN as well.

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Last-modified: 2023-03-25 (土) 11:19:17