annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.

AuthorTim Yates <Tim.Yates@cruk.manchester.ac.uk>
Date of publicationNone
MaintainerChris Wirth <Christopher.Wirth@cruk.manchester.ac.uk>
LicenseGPL-2
Version1.16.0
http://annmap.cruk.manchester.ac.uk

View on Bioconductor

Files in this package

annmap/.BBSoptions
annmap/DESCRIPTION
annmap/NAMESPACE
annmap/R
annmap/R/cache.R annmap/R/coords.R annmap/R/db.R annmap/R/filtering.R annmap/R/plot.genomic.R annmap/R/plot.ngs.R annmap/R/si.R annmap/R/statements.R annmap/R/utils.R annmap/R/utr.R annmap/R/ws.R annmap/R/zzz.R
annmap/build
annmap/build/vignette.rds
annmap/inst
annmap/inst/NEWS.Rd
annmap/inst/README
annmap/inst/cookbook
annmap/inst/cookbook/Sweave.sty
annmap/inst/cookbook/cookbook.Rnw
annmap/inst/cookbook/delia.R
annmap/inst/cookbook/yellow-exclamation.png
annmap/inst/databases.txt
annmap/inst/doc
annmap/inst/doc/INSTALL.Rnw
annmap/inst/doc/INSTALL.pdf
annmap/inst/doc/annmap.Rnw
annmap/inst/doc/annmap.pdf
annmap/inst/doc/cookbook.Rnw
annmap/inst/doc/cookbook.pdf
annmap/inst/ngsGridPlotExample.R
annmap/inst/rdata
annmap/inst/rdata/HG-U133Plus2.tp53.expr.RData
annmap/inst/rdata/HuEx-1_0.tp53.expr.RData
annmap/inst/unitTests
annmap/inst/unitTests/Makefile
annmap/inst/unitTests/commaConfig
annmap/inst/unitTests/commaConfig/databases.txt
annmap/inst/unitTests/runit.TEMPLATE.R
annmap/inst/unitTests/runit.all-statements.R
annmap/inst/unitTests/runit.cache.R
annmap/inst/unitTests/runit.coords.R
annmap/inst/unitTests/runit.data.R
annmap/inst/unitTests/runit.db.R
annmap/inst/unitTests/runit.detail-statements.R
annmap/inst/unitTests/runit.extras.R
annmap/inst/unitTests/runit.plots.R
annmap/inst/unitTests/runit.range-statements.R
annmap/inst/unitTests/runit.to-statements.R
annmap/inst/unitTests/runit.utils.R
annmap/inst/unitTests/runit.utr.R
annmap/inst/unitTests/runit.ws.R
annmap/inst/unitTests/tabConfig
annmap/inst/unitTests/tabConfig/databases.txt
annmap/man
annmap/man/annmap-package.Rd annmap/man/annmap.all.Rd annmap/man/annmap.coords.Rd annmap/man/annmap.details.Rd annmap/man/annmap.env.Rd annmap/man/annmap.filters.Rd annmap/man/annmap.range.Rd annmap/man/annmap.seqname.Rd annmap/man/annmap.spliceIndex.Rd annmap/man/annmap.to.Rd annmap/man/annmap.utils.Rd annmap/man/annmap.utr.Rd annmap/man/plot.genomic.Rd annmap/man/plot.ngs.Rd
annmap/tests
annmap/tests/doRUnit.R
annmap/vignettes
annmap/vignettes/INSTALL.Rnw
annmap/vignettes/Makefile
annmap/vignettes/annmap.Rnw
annmap/vignettes/cookbook.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.