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

Share:

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.

Author
Tim Yates <Tim.Yates@cruk.manchester.ac.uk>
Date of publication
None
Maintainer
Chris Wirth <Christopher.Wirth@cruk.manchester.ac.uk>
License
GPL-2
Version
1.16.0
URLs

View on Bioconductor

Man pages

annmap.all
annmap 'all' functions
annmap.coords
annmap co-ordinate mapping functions
annmap.details
annmap 'details' functions
annmap.env
annmap 'env' functions
annmap.filters
annmap 'filter' functions
annmap-package
Provide access to the Annmap annotation database
annmap.range
annmap 'range' functions
annmap.seqname
Seqnames manipulation functions
annmap.spliceIndex
Splice indexing
annmap.to
annmap 'to' functions
annmap.utils
annmap 'utils' functions
annmap.utr
annmap coding functions
plot.genomic
Plotting a section of a chromosome.
plot.ngs
Plotting BAM file data alongside the features of a chromosome

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