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annotationTools (version 1.46.0)

Annotate microarrays and perform cross-species gene expression analyses using flat file databases.

Description

Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).

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Version

Version

1.46.0

License

GPL

Maintainer

Alexandre Kuhn

Last Published

February 15th, 2017

Functions in annotationTools (1.46.0)

compactList

Concatenate list elements
homologene_part

Example HomoloGene file
HG-U133_Plus_2_annot_part

Example Affymetrix annotation file
listToCharacterVector

Turn list into character vector
getGENESYMBOL

Find gene symbols
getOrthologousProbesets

Find orthologous/homologous probe sets present in a target set using a mapping table
getANNOTATION

General annotation function
getHOMOLOG

Find homologous/orthologous gene (ID)
getGENEONTOLOGY

Find Gene Ontology (GO) annotation
getMULTIANNOTATION

General (multiple) annotation function
getGENETITLE

Find gene titles
HG-U133_Plus_2_ortholog_part

Example Affymetrix ortholog file
table_human

table\_human
ortho

ortho
getPROBESET

Find probe set IDs
ps2ps

Find orthologous/homologous probe sets across two different Affymetrix microarray formats using HomoloGene
table_mouse

table\_mouse
getGENEID

Find gene IDs
annot_HGU133A

annot\_HGU133A
Mouse430_2_annot_part

Example Affymetrix annotation file