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Bioconductor
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Installed Bioconductor
packages include:
- General tools:
- Biobase:
Object-oriented representation
and manipulation of genomic data (S4 class structure).
- tkWidgets:
Tools for creating Tcl/Tk widgets, i.e., small-scale graphical
user interfaces.
- Annotation:
- 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.
- AnnBuilder: Assemble and process
genomic annotation data, from databases such as GenBank, the
Gene Ontology Consortium, LocusLink, UniGene, the UCSC Human
Genome Project.
- Graphics:
- geneplotter: Graphical
tools for genomic data, for example for plotting expression
data along a chromosome or producing color images of expression
data matrices
- Pre-processing:
- affy:
Diagnostic plots, expression measures, and normalization for
Affymetrix chip data.
marryClasses, marryInput, marryNorm, marryPlots: Diagnostic
plots and normalization for cDNA microarray data.
- Differential gene expression:
- 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.
- 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.
ROC: Receiver Operating Characteristic (ROC) approach for
identifying genes that are differentially expressed int two
types of samples.
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(c) SJava - An Omegahat R Package
A package that provides direct access to calling
arbitrary Java methods and creating arbitrary Java objects from
within R and also calling R functions from Java. This can be
used to get access to network facilities; create graphical interfaces
with R functions as callbacks; image manipulation classes; mail
package; etc.
http://cran.r-project.org/
"Source of contributed packages"
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