1 Introduction | 2 Annotation | 3 Find orthologs | 4 Build tables of orthologous probe sets | 5 An example cross-species analysis of gene expression: Transcriptional dysregulation in Huntington's disease patients and in a genetic mouse model | 6 Session Information
Package: annotationTools 1.87.0
Alexandre Kuhn
annotationTools: Annotate microarrays and perform cross-species gene expression analyses using flat file databases
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).
Authors:
annotationTools_1.87.0.tar.gz
annotationTools_1.87.0.zip(r-4.7)annotationTools_1.87.0.zip(r-4.6)annotationTools_1.87.0.zip(r-4.5)
annotationTools_1.87.0.tgz(r-4.6-any)annotationTools_1.87.0.tgz(r-4.5-any)
annotationTools_1.87.0.tar.gz(r-4.7-any)annotationTools_1.87.0.tar.gz(r-4.6-any)
annotationTools_1.87.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
annotationTools/json (API)
| # Install 'annotationTools' in R: |
| install.packages('annotationTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- annot_HGU133A - Annot\_HGU133A
- ortho - Ortho
- table_human - Table\_human
- table_mouse - Table\_mouse
On BioConductor:annotationTools-1.87.0(bioc 3.24)annotationTools-1.86.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:f13657d7c8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 146 | ||
| linux-devel-x86_64 | NOTE | 205 | ||
| source / vignettes | OK | 262 | ||
| linux-release-x86_64 | NOTE | 197 | ||
| macos-release-arm64 | NOTE | 104 | ||
| macos-oldrel-arm64 | NOTE | 90 | ||
| windows-devel | NOTE | 79 | ||
| windows-release | NOTE | 82 | ||
| windows-oldrel | NOTE | 81 | ||
| wasm-release | OK | 130 |
Exports:compactListgetANNOTATIONgetGENEIDgetGENEONTOLOGYgetGENESYMBOLgetGENETITLEgetHOMOLOGgetMULTIANNOTATIONgetOrthologousProbesetsgetPROBESETlistToCharacterVectorps2ps
Dependencies:BiobaseBiocGenericsgenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| annot\_HGU133A | annot_HGU133A |
| Concatenate list elements | compactList |
| Example gene_orthologs file | gene_orthologs_part |
| General annotation function | getANNOTATION |
| Find gene IDs | getGENEID |
| Find Gene Ontology (GO) annotation | getGENEONTOLOGY |
| Find gene symbols | getGENESYMBOL |
| Find gene titles | getGENETITLE |
| Find homologous/orthologous gene (ID) | getHOMOLOG |
| General (multiple) annotation function | getMULTIANNOTATION |
| Find orthologous/homologous probe sets present in a target set using a mapping table | getOrthologousProbesets |
| Find probe set IDs | getPROBESET |
| Example Affymetrix annotation file | HG-U133_Plus_2_annot_part |
| Example Affymetrix ortholog file | HG-U133_Plus_2_ortholog_part |
| Example HomoloGene file | homologene_part |
| Turn list into character vector | listToCharacterVector |
| Example Affymetrix annotation file | Mouse430_2_annot_part |
| ortho | ortho |
| Find orthologous/homologous probe sets across two different Affymetrix microarray formats using a table of orthologs | ps2ps |
| table\_human | table_human |
| table\_mouse | table_mouse |
