Package |
Maintainer |
Title |
affycoretools
|
James W. MacDonald |
Functions useful for those doing repetitive analyses with
Affymetrix GeneChips. |
AffyExpress
|
Xuejun Arthur Li |
Affymetrix Quality Assessment and Analysis Tool |
altcdfenvs
|
Laurent Gautier |
alternative CDF environments (aka mappings) |
annaffy
|
Colin A. Smith |
Annotation tools for Affymetrix biological metadata |
AnnBuilder
|
J. Zhang |
Bioconductor annotation data package builder |
annotate
|
Biocore Team c/o BioC user list
|
Annotation for microarrays |
AnnotationDbi
|
Biocore Team c/o BioC user list
|
Annotation Database Interface |
annotationTools
|
Alexandre Kuhn |
Annotate microarrays and perform cross-species gene expression
analyses using flat file databases. |
arrayQualityMetrics
|
Audrey Kauffmann |
Quality metrics on microarray data sets |
biomaRt
|
Steffen Durinck |
Interface to BioMart databases (e.g. Ensembl, Wormbase and
Gramene) |
Category
|
Robert Gentleman |
Category Analysis |
DynDoc
|
Biocore Team c/o BioC user list
|
Dynamic document tools |
ecolitk
|
Laurent |
Meta-data and tools for E. coli |
exonmap
|
Crispin Miller |
High level analysis of Affymetrix exon array data |
gaggle
|
Dan Tenenbaum |
Broadcast data between R and Java bioinformatics programs |
GeneR
|
Y. d'Aubenton-Carafa |
R for genes and sequences analysis |
GeneRfold
|
Antoine Lucas |
R for genes and sequences, using viennaRNA package (fold) |
GlobalAncova
|
R. Meister |
Calculates a global test for differential gene expression
between groups |
globaltest
|
Jelle Goeman |
Testing Association of Groups of Genes with a Clinical Variable |
goProfiles
|
Alex Sanchez |
goProfiles: an R package for the statistical analysis of
functional profiles |
GOstats
|
Robert Gentleman |
Tools for manipulating GO and microarrays. |
goTools
|
Agnes Paquet |
Functions for Gene Ontology database |
KEGGSOAP
|
Robert Gentleman |
Client-side SOAP access KEGG |
matchprobes
|
Biocore Team c/o BioC user list
|
Basic infrastructure for using oligonucleotide microarray
reporter sequence information for preprocessing and quality
assessment |
nem
|
Florian Markowetz |
Nested Effects Models to reconstruct phenotypic hierarchies |
occugene
|
Oliver Will |
Functions for Multinomial Occupancy Distribution |
pdInfoBuilder
|
Benilton Carvalho |
Platform Design Information Package Builder |
Resourcerer
|
Jianhua Zhang |
Reads annotation data from TIGR Resourcerer or convert the
annotation data into Bioconductor data pacakge. |
RSNPper
|
VJ Carey |
interface to chip.org::SNPper for SNP-related data |
rtracklayer
|
Michael Lawrence |
R interface to genome browsers and their annotation tracks |
SemSim
|
Xiang Guo |
Gene Ontology-based Semantic Similarity Measures |
simpleaffy
|
Crispin Miller |
Very simple high level analysis of Affymetrix data |